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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 110
 111                 else {
 112                         vector<string> myArray = setParameters();
 113
 114                         OptionParser parser(option);
 115                         map<string, string> parameters = parser.getParameters();
 116
 117                         ValidParameters validParameter("classify.seqs");
 118                         map<string, string>::iterator it;
 119
 120                         //check to make sure all parameters are valid for command
 121                         for (it = parameters.begin(); it != parameters.end(); it++) {
 122                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 123                         }
 124
 125                         //initialize outputTypes
 126                         vector<string> tempOutNames;
 127                         outputTypes["taxonomy"] = tempOutNames;
 128                         outputTypes["taxsummary"] = tempOutNames;
 129                         outputTypes["matchdist"] = tempOutNames;
 130
 131                         //if the user changes the output directory command factory will send this info to us in the output parameter
 132                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 133
 134                         //if the user changes the input directory command factory will send this info to us in the output parameter
 135                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 136                         if (inputDir == "not found"){   inputDir = "";          }
 137                         else {
 138                                 string path;
 139                                 it = parameters.find("reference");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 145                                 }
 146
 147                                 it = parameters.find("taxonomy");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 153                                 }
 154
 155                                 it = parameters.find("group");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 161                                 }
 162                         }
 163
 164                         //check for required parameters
 165                         templateFileName = validParameter.validFile(parameters, "reference", true);
 166                         if (templateFileName == "not found") {
 167                                 m->mothurOut("reference is a required parameter for the classify.seqs command.");
 168                                 m->mothurOutEndLine();
 169                                 abort = true;
 170                         }
 171                         else if (templateFileName == "not open") { abort = true; }
 172
 173
 174                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 175                         if (fastaFileName == "not found") {
 176                                 //if there is a current fasta file, use it
 177                                 string filename = m->getFastaFile();
 178                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 179                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 180                         }
 181                         else {
 182                                 m->splitAtDash(fastaFileName, fastaFileNames);
 183
 184                                 //go through files and make sure they are good, if not, then disregard them
 185                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 186
 187                                         bool ignore = false;
 188                                         if (fastaFileNames[i] == "current") {
 189                                                 fastaFileNames[i] = m->getFastaFile();
 190                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 191                                                 else {
 192                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 193                                                         //erase from file list
 194                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 195                                                         i--;
 196                                                 }
 197                                         }
 198
 199                                         if (!ignore) {
 200
 201                                                 if (inputDir != "") {
 202                                                         string path = m->hasPath(fastaFileNames[i]);
 203                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 204                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 205                                                 }
 206
 207                                                 int ableToOpen;
 208
 209                                                 ifstream in;
 210                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 211
 212                                                 //if you can't open it, try default location
 213                                                 if (ableToOpen == 1) {
 214                                                         if (m->getDefaultPath() != "") { //default path is set
 215                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 216                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 217                                                                 ifstream in2;
 218                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 219                                                                 in2.close();
 220                                                                 fastaFileNames[i] = tryPath;
 221                                                         }
 222                                                 }
 223
 224                                                 if (ableToOpen == 1) {
 225                                                         if (m->getOutputDir() != "") { //default path is set
 226                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 227                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 228                                                                 ifstream in2;
 229                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 230                                                                 in2.close();
 231                                                                 fastaFileNames[i] = tryPath;
 232                                                         }
 233                                                 }
 234
 235                                                 in.close();
 236
 237                                                 if (ableToOpen == 1) {
 238                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 239                                                         //erase from file list
 240                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 241                                                         i--;
 242                                                 }
 243                                         }
 244
 245                                 }
 246
 247                                 //make sure there is at least one valid file left
 248                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 249                         }
 250
 251
 252                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 253                         if (taxonomyFileName == "not found") {
 254                                 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
 255                                 m->mothurOutEndLine();
 256                                 abort = true;
 257                         }
 258                         else if (taxonomyFileName == "not open") { abort = true; }
 259
 260
 261                         namefile = validParameter.validFile(parameters, "name", false);
 262                         if (namefile == "not found") { namefile = "";  }
 263
 264                         else {
 265                                 m->splitAtDash(namefile, namefileNames);
 266
 267                                 //go through files and make sure they are good, if not, then disregard them
 268                                 for (int i = 0; i < namefileNames.size(); i++) {
 269                                         bool ignore = false;
 270                                         if (namefileNames[i] == "current") {
 271                                                 namefileNames[i] = m->getNameFile();
 272                                                 if (namefileNames[i] != "") {  m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 273                                                 else {
 274                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 275                                                         //erase from file list
 276                                                         namefileNames.erase(namefileNames.begin()+i);
 277                                                         i--;
 278                                                 }
 279                                         }
 280
 281                                         if (!ignore) {
 282
 283                                                 if (inputDir != "") {
 284                                                         string path = m->hasPath(namefileNames[i]);
 285                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 286                                                         if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 287                                                 }
 288                                                 int ableToOpen;
 289
 290                                                 ifstream in;
 291                                                 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 292
 293                                                 //if you can't open it, try default location
 294                                                 if (ableToOpen == 1) {
 295                                                         if (m->getDefaultPath() != "") { //default path is set
 296                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 297                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 298                                                                 ifstream in2;
 299                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 300                                                                 in2.close();
 301                                                                 namefileNames[i] = tryPath;
 302                                                         }
 303                                                 }
 304
 305                                                 if (ableToOpen == 1) {
 306                                                         if (m->getOutputDir() != "") { //default path is set
 307                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 308                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 309                                                                 ifstream in2;
 310                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 311                                                                 in2.close();
 312                                                                 namefileNames[i] = tryPath;
 313                                                         }
 314                                                 }
 315                                                 in.close();
 316
 317                                                 if (ableToOpen == 1) {
 318                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 319                                                         //erase from file list
 320                                                         namefileNames.erase(namefileNames.begin()+i);
 321                                                         i--;
 322                                                 }
 323                                         }
 324                                 }
 325                         }
 326
 327                         if (namefile != "") {
 328                                 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(); }
 329                         }
 330
 331                         groupfile = validParameter.validFile(parameters, "group", false);
 332                         if (groupfile == "not found") { groupfile = "";  }
 333                         else {
 334                                 m->splitAtDash(groupfile, groupfileNames);
 335
 336                                 //go through files and make sure they are good, if not, then disregard them
 337                                 for (int i = 0; i < groupfileNames.size(); i++) {
 338                                         if (inputDir != "") {
 339                                                 string path = m->hasPath(groupfileNames[i]);
 340                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 341                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 342                                         }
 343                                         int ableToOpen;
 344
 345                                         ifstream in;
 346                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 347
 348                                         //if you can't open it, try default location
 349                                         if (ableToOpen == 1) {
 350                                                 if (m->getDefaultPath() != "") { //default path is set
 351                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 352                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 353                                                         ifstream in2;
 354                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 355                                                         in2.close();
 356                                                         groupfileNames[i] = tryPath;
 357                                                 }
 358                                         }
 359
 360                                         if (ableToOpen == 1) {
 361                                                 if (m->getOutputDir() != "") { //default path is set
 362                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 363                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 364                                                         ifstream in2;
 365                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 366                                                         in2.close();
 367                                                         groupfileNames[i] = tryPath;
 368                                                 }
 369                                         }
 370
 371                                         in.close();
 372
 373                                         if (ableToOpen == 1) {
 374                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 375                                                 //erase from file list
 376                                                 groupfileNames.erase(groupfileNames.begin()+i);
 377                                                 i--;
 378                                         }
 379                                 }
 380                         }
 381
 382                         if (groupfile != "") {
 383                                 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(); }
 384                         }else {
 385                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 386                         }
 387
 388                         //check for optional parameter and set defaults
 389                         // ...at some point should added some additional type checking...
 390                         string temp;
 391                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 392                         convert(temp, kmerSize);
 393
 394                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 395                         m->setProcessors(temp);
 396                         convert(temp, processors);
 397
 398                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 399
 400                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 401
 402                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 403                         convert(temp, match);
 404
 405                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 406                         convert(temp, misMatch);
 407
 408                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 409                         convert(temp, gapOpen);
 410
 411                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 412                         convert(temp, gapExtend);
 413
 414                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 415                         convert(temp, numWanted);
 416
 417                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 418                         convert(temp, cutoff);
 419
 420                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 421                         probs = m->isTrue(temp);
 422
 423                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 424                         convert(temp, iters);
 425
 426
 427
 428                         if ((method == "bayesian") && (search != "kmer"))  {
 429                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 430                                 search = "kmer";
 431                         }
 432                 }
 433
 434         }
 435         catch(exception& e) {
 436                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 437                 exit(1);
 438         }
 439 }
 440
 441 //**********************************************************************************************************************
 442 ClassifySeqsCommand::~ClassifySeqsCommand(){
 443         if (abort == false) {
 444                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 445         }
 446 }
 447 //**********************************************************************************************************************
 448
 449 int ClassifySeqsCommand::execute(){
 450         try {
 451                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 452
 453                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
 454                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
 455                 else {
 456                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 457                         m->mothurOutEndLine();
 458                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
 459                 }
 460
 461                 if (m->control_pressed) { delete classify; return 0; }
 462
 463
 464                 for (int s = 0; s < fastaFileNames.size(); s++) {
 465
 466                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 467
 468                         string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
 469                         RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
 470                         if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
 471                         RippedTaxName +=  ".";
 472
 473                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 474                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 475                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 476                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
 477
 478                         if ((method == "knn") && (search == "distance")) {
 479                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
 480                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 481                         }
 482
 483                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 484                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 485
 486                         int start = time(NULL);
 487                         int numFastaSeqs = 0;
 488                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 489
 490 #ifdef USE_MPI
 491                                 int pid, numSeqsPerProcessor;
 492                                 int tag = 2001;
 493                                 vector<unsigned long int> MPIPos;
 494
 495                                 MPI_Status status;
 496                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 497                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 498
 499                                 MPI_File inMPI;
 500                                 MPI_File outMPINewTax;
 501                                 MPI_File outMPITempTax;
 502
 503                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 504                                 int inMode=MPI_MODE_RDONLY;
 505
 506                                 char outNewTax[1024];
 507                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 508
 509                                 char outTempTax[1024];
 510                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 511
 512                                 char inFileName[1024];
 513                                 strcpy(inFileName, fastaFileNames[s].c_str());
 514
 515                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 516                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 517                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 518
 519                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 520
 521                                 if (pid == 0) { //you are the root process
 522
 523                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 524
 525                                         //send file positions to all processes
 526                                         for(int i = 1; i < processors; i++) {
 527                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 528                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 529                                         }
 530
 531                                         //figure out how many sequences you have to align
 532                                         numSeqsPerProcessor = numFastaSeqs / processors;
 533                                         int startIndex =  pid * numSeqsPerProcessor;
 534                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 535
 536
 537                                         //align your part
 538                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 539
 540                                         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;  }
 541
 542                                         for (int i = 1; i < processors; i++) {
 543                                                 int done;
 544                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 545                                         }
 546                                 }else{ //you are a child process
 547                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 548                                         MPIPos.resize(numFastaSeqs+1);
 549                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 550
 551                                         //figure out how many sequences you have to align
 552                                         numSeqsPerProcessor = numFastaSeqs / processors;
 553                                         int startIndex =  pid * numSeqsPerProcessor;
 554                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 555
 556
 557                                         //align your part
 558                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 559
 560                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 561
 562                                         int done = 0;
 563                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 564                                 }
 565
 566                                 //close files
 567                                 MPI_File_close(&inMPI);
 568                                 MPI_File_close(&outMPINewTax);
 569                                 MPI_File_close(&outMPITempTax);
 570                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 571
 572 #else
 573
 574                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 575
 576                         for (int i = 0; i < (positions.size()-1); i++) {
 577                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 578                         }
 579
 580                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 581                         if(processors == 1){
 582                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 583                         }
 584                         else{
 585                                 processIDS.resize(0);
 586
 587                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 588
 589                         }
 590         #else
 591                         numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 592         #endif
 593 #endif
 594
 595                 m->mothurOutEndLine();
 596                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 597                 start = time(NULL);
 598
 599
 600                 #ifdef USE_MPI
 601                         if (pid == 0) {  //this part does not need to be paralellized
 602
 603                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 604                 #else
 605                         //read namefile
 606                         if(namefile != "") {
 607
 608                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 609
 610                                 nameMap.clear(); //remove old names
 611
 612                                 ifstream inNames;
 613                                 m->openInputFile(namefileNames[s], inNames);
 614
 615                                 string firstCol, secondCol;
 616                                 while(!inNames.eof()) {
 617                                         inNames >> firstCol >> secondCol; m->gobble(inNames);
 618
 619                                         vector<string> temp;
 620                                         m->splitAtComma(secondCol, temp);
 621
 622                                         nameMap[firstCol] = temp;
 623                                 }
 624                                 inNames.close();
 625
 626                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 627                         }
 628                 #endif
 629
 630                         string group = "";
 631                         if (groupfile != "") {  group = groupfileNames[s]; }
 632
 633                         PhyloSummary taxaSum(taxonomyFileName, group);
 634
 635                         if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 636
 637                         if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
 638                         else {
 639                                 ifstream in;
 640                                 m->openInputFile(tempTaxonomyFile, in);
 641
 642                                 //read in users taxonomy file and add sequences to tree
 643                                 string name, taxon;
 644
 645                                 while(!in.eof()){
 646                                         in >> name >> taxon; m->gobble(in);
 647
 648                                         itNames = nameMap.find(name);
 649
 650                                         if (itNames == nameMap.end()) {
 651                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 652                                         }else{
 653                                                 for (int i = 0; i < itNames->second.size(); i++) {
 654                                                         taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 655                                                 }
 656                                                 itNames->second.clear();
 657                                                 nameMap.erase(itNames->first);
 658                                         }
 659                                 }
 660                                 in.close();
 661                         }
 662                         remove(tempTaxonomyFile.c_str());
 663
 664                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 665
 666                         //print summary file
 667                         ofstream outTaxTree;
 668                         m->openOutputFile(taxSummary, outTaxTree);
 669                         taxaSum.print(outTaxTree);
 670                         outTaxTree.close();
 671
 672                         //output taxonomy with the unclassified bins added
 673                         ifstream inTax;
 674                         m->openInputFile(newTaxonomyFile, inTax);
 675
 676                         ofstream outTax;
 677                         string unclass = newTaxonomyFile + ".unclass.temp";
 678                         m->openOutputFile(unclass, outTax);
 679
 680                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 681                         int maxLevel = taxaSum.getMaxLevel();
 682
 683                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 684                         string name, taxon;
 685                         while (!inTax.eof()) {
 686                                 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; }
 687
 688                                 inTax >> name >> taxon; m->gobble(inTax);
 689
 690                                 string newTax = addUnclassifieds(taxon, maxLevel);
 691
 692                                 outTax << name << '\t' << newTax << endl;
 693                         }
 694                         inTax.close();
 695                         outTax.close();
 696
 697                         remove(newTaxonomyFile.c_str());
 698                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 699
 700                         m->mothurOutEndLine();
 701                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 702
 703                         #ifdef USE_MPI
 704                                 }
 705                         #endif
 706
 707                         m->mothurOutEndLine();
 708                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 709                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 710                         m->mothurOutEndLine();
 711                 }
 712
 713                 //set taxonomy file as new current taxonomyfile
 714                 string current = "";
 715                 itTypes = outputTypes.find("taxonomy");
 716                 if (itTypes != outputTypes.end()) {
 717                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 718                 }
 719
 720                 delete classify;
 721                 return 0;
 722         }
 723         catch(exception& e) {
 724                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 725                 exit(1);
 726         }
 727 }
 728
 729 /**************************************************************************************************/
 730 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 731         try{
 732                 string newTax, taxon;
 733                 int level = 0;
 734
 735                 //keep what you have counting the levels
 736                 while (tax.find_first_of(';') != -1) {
 737                         //get taxon
 738                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 739                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 740                         newTax += taxon;
 741                         level++;
 742                 }
 743
 744                 //add "unclassified" until you reach maxLevel
 745                 while (level < maxlevel) {
 746                         newTax += "unclassified;";
 747                         level++;
 748                 }
 749
 750                 return newTax;
 751         }
 752         catch(exception& e) {
 753                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 754                 exit(1);
 755         }
 756 }
 757
 758 /**************************************************************************************************/
 759
 760 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
 761         try {
 762 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 763                 int process = 1;
 764                 int num = 0;
 765
 766                 //loop through and create all the processes you want
 767                 while (process != processors) {
 768                         int pid = fork();
 769
 770                         if (pid > 0) {
 771                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 772                                 process++;
 773                         }else if (pid == 0){
 774                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
 775
 776                                 //pass numSeqs to parent
 777                                 ofstream out;
 778                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 779                                 m->openOutputFile(tempFile, out);
 780                                 out << num << endl;
 781                                 out.close();
 782
 783                                 exit(0);
 784                         }else {
 785                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 786                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 787                                 exit(0);
 788                         }
 789                 }
 790
 791                 //parent does its part
 792                 num = driver(lines[0], taxFileName, tempTaxFile, filename);
 793
 794                 //force parent to wait until all the processes are done
 795                 for (int i=0;i<processIDS.size();i++) {
 796                         int temp = processIDS[i];
 797                         wait(&temp);
 798                 }
 799
 800                 for (int i = 0; i < processIDS.size(); i++) {
 801                         ifstream in;
 802                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 803                         m->openInputFile(tempFile, in);
 804                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 805                         in.close(); remove(tempFile.c_str());
 806                 }
 807
 808                 for(int i=0;i<processIDS.size();i++){
 809                         appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 810                         appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
 811                         remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
 812                         remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
 813                 }
 814
 815                 return num;
 816 #endif
 817         }
 818         catch(exception& e) {
 819                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 820                 exit(1);
 821         }
 822 }
 823 /**************************************************************************************************/
 824
 825 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
 826         try{
 827
 828                 ofstream output;
 829                 ifstream input;
 830                 m->openOutputFileAppend(filename, output);
 831                 m->openInputFile(temp, input);
 832
 833                 while(char c = input.get()){
 834                         if(input.eof())         {       break;                  }
 835                         else                            {       output << c;    }
 836                 }
 837
 838                 input.close();
 839                 output.close();
 840         }
 841         catch(exception& e) {
 842                 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
 843                 exit(1);
 844         }
 845 }
 846
 847 //**********************************************************************************************************************
 848
 849 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
 850         try {
 851                 ofstream outTax;
 852                 m->openOutputFile(taxFName, outTax);
 853
 854                 ofstream outTaxSimple;
 855                 m->openOutputFile(tempTFName, outTaxSimple);
 856
 857                 ifstream inFASTA;
 858                 m->openInputFile(filename, inFASTA);
 859
 860                 string taxonomy;
 861
 862                 inFASTA.seekg(filePos->start);
 863
 864                 bool done = false;
 865                 int count = 0;
 866
 867                 while (!done) {
 868                         if (m->control_pressed) { return 0; }
 869
 870                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
 871
 872                         if (candidateSeq->getName() != "") {
 873
 874                                 taxonomy = classify->getTaxonomy(candidateSeq);
 875
 876                                 if (m->control_pressed) { delete candidateSeq; return 0; }
 877
 878                                 if (taxonomy != "bad seq") {
 879                                         //output confidence scores or not
 880                                         if (probs) {
 881                                                 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
 882                                         }else{
 883                                                 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 884                                         }
 885
 886                                         outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 887                                 }
 888                                 count++;
 889                         }
 890                         delete candidateSeq;
 891
 892                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 893                                 unsigned long int pos = inFASTA.tellg();
 894                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 895                         #else
 896                                 if (inFASTA.eof()) { break; }
 897                         #endif
 898
 899                         //report progress
 900                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 901
 902                 }
 903                 //report progress
 904                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 905
 906                 inFASTA.close();
 907                 outTax.close();
 908                 outTaxSimple.close();
 909
 910                 return count;
 911         }
 912         catch(exception& e) {
 913                 m->errorOut(e, "ClassifySeqsCommand", "driver");
 914                 exit(1);
 915         }
 916 }
 917 //**********************************************************************************************************************
 918 #ifdef USE_MPI
 919 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
 920         try {
 921                 MPI_Status statusNew;
 922                 MPI_Status statusTemp;
 923                 MPI_Status status;
 924
 925                 int pid;
 926                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 927
 928                 string taxonomy;
 929                 string outputString;
 930
 931                 for(int i=0;i<num;i++){
 932
 933                         if (m->control_pressed) { return 0; }
 934
 935                         //read next sequence
 936                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 937                         char* buf4 = new char[length];
 938                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 939
 940                         string tempBuf = buf4;
 941                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 942                         istringstream iss (tempBuf,istringstream::in);
 943                         delete buf4;
 944
 945                         Sequence* candidateSeq = new Sequence(iss);
 946
 947                         if (candidateSeq->getName() != "") {
 948                                 taxonomy = classify->getTaxonomy(candidateSeq);
 949
 950                                 if (taxonomy != "bad seq") {
 951                                         //output confidence scores or not
 952                                         if (probs) {
 953                                                 outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
 954                                         }else{
 955                                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 956                                         }
 957
 958                                         int length = outputString.length();
 959                                         char* buf2 = new char[length];
 960                                         memcpy(buf2, outputString.c_str(), length);
 961
 962                                         MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
 963                                         delete buf2;
 964
 965                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 966                                         length = outputString.length();
 967                                         char* buf = new char[length];
 968                                         memcpy(buf, outputString.c_str(), length);
 969
 970                                         MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
 971                                         delete buf;
 972                                 }
 973                         }
 974                         delete candidateSeq;
 975
 976                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
 977                 }
 978
 979                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
 980
 981
 982                 return 1;
 983         }
 984         catch(exception& e) {
 985                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
 986                 exit(1);
 987         }
 988 }
 989
 990 //**********************************************************************************************************************
 991 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
 992         try {
 993
 994                 nameMap.clear(); //remove old names
 995
 996                 MPI_File inMPI;
 997                 MPI_Offset size;
 998                 MPI_Status status;
 999
1000                 //char* inFileName = new char[nameFilename.length()];
1001                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1002
1003                 char inFileName[1024];
1004                 strcpy(inFileName, nameFilename.c_str());
1005
1006                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1007                 MPI_File_get_size(inMPI, &size);
1008                 //delete inFileName;
1009
1010                 char* buffer = new char[size];
1011                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1012
1013                 string tempBuf = buffer;
1014                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
1015                 istringstream iss (tempBuf,istringstream::in);
1016                 delete buffer;
1017
1018                 string firstCol, secondCol;
1019                 while(!iss.eof()) {
1020                         iss >> firstCol >> secondCol; m->gobble(iss);
1021
1022                         vector<string> temp;
1023                         m->splitAtComma(secondCol, temp);
1024
1025                         nameMap[firstCol] = temp;
1026                 }
1027
1028                 MPI_File_close(&inMPI);
1029
1030                 return 1;
1031         }
1032         catch(exception& e) {
1033                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1034                 exit(1);
1035         }
1036 }
1037 #endif
1038 /**************************************************************************************************/