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                                                 }else {
 243                                                         m->setFastaFile(fastaFileNames[i]);
 244                                                 }
 245                                         }
 246
 247                                 }
 248
 249                                 //make sure there is at least one valid file left
 250                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 251                         }
 252
 253
 254                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 255                         if (taxonomyFileName == "not found") {
 256                                 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
 257                                 m->mothurOutEndLine();
 258                                 abort = true;
 259                         }
 260                         else if (taxonomyFileName == "not open") { abort = true; }
 261
 262
 263                         namefile = validParameter.validFile(parameters, "name", false);
 264                         if (namefile == "not found") { namefile = "";  }
 265
 266                         else {
 267                                 m->splitAtDash(namefile, namefileNames);
 268
 269                                 //go through files and make sure they are good, if not, then disregard them
 270                                 for (int i = 0; i < namefileNames.size(); i++) {
 271                                         bool ignore = false;
 272                                         if (namefileNames[i] == "current") {
 273                                                 namefileNames[i] = m->getNameFile();
 274                                                 if (namefileNames[i] != "") {  m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 275                                                 else {
 276                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 277                                                         //erase from file list
 278                                                         namefileNames.erase(namefileNames.begin()+i);
 279                                                         i--;
 280                                                 }
 281                                         }
 282
 283                                         if (!ignore) {
 284
 285                                                 if (inputDir != "") {
 286                                                         string path = m->hasPath(namefileNames[i]);
 287                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 288                                                         if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 289                                                 }
 290                                                 int ableToOpen;
 291
 292                                                 ifstream in;
 293                                                 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 294
 295                                                 //if you can't open it, try default location
 296                                                 if (ableToOpen == 1) {
 297                                                         if (m->getDefaultPath() != "") { //default path is set
 298                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 299                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 300                                                                 ifstream in2;
 301                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 302                                                                 in2.close();
 303                                                                 namefileNames[i] = tryPath;
 304                                                         }
 305                                                 }
 306
 307                                                 if (ableToOpen == 1) {
 308                                                         if (m->getOutputDir() != "") { //default path is set
 309                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 310                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 311                                                                 ifstream in2;
 312                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 313                                                                 in2.close();
 314                                                                 namefileNames[i] = tryPath;
 315                                                         }
 316                                                 }
 317                                                 in.close();
 318
 319                                                 if (ableToOpen == 1) {
 320                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 321                                                         //erase from file list
 322                                                         namefileNames.erase(namefileNames.begin()+i);
 323                                                         i--;
 324                                                 }else {
 325                                                         m->setNameFile(namefileNames[i]);
 326                                                 }
 327                                         }
 328                                 }
 329                         }
 330
 331                         if (namefile != "") {
 332                                 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(); }
 333                         }
 334
 335                         groupfile = validParameter.validFile(parameters, "group", false);
 336                         if (groupfile == "not found") { groupfile = "";  }
 337                         else {
 338                                 m->splitAtDash(groupfile, groupfileNames);
 339
 340                                 //go through files and make sure they are good, if not, then disregard them
 341                                 for (int i = 0; i < groupfileNames.size(); i++) {
 342                                         if (inputDir != "") {
 343                                                 string path = m->hasPath(groupfileNames[i]);
 344                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 345                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 346                                         }
 347                                         int ableToOpen;
 348
 349                                         ifstream in;
 350                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 351
 352                                         //if you can't open it, try default location
 353                                         if (ableToOpen == 1) {
 354                                                 if (m->getDefaultPath() != "") { //default path is set
 355                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 356                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 357                                                         ifstream in2;
 358                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 359                                                         in2.close();
 360                                                         groupfileNames[i] = tryPath;
 361                                                 }
 362                                         }
 363
 364                                         if (ableToOpen == 1) {
 365                                                 if (m->getOutputDir() != "") { //default path is set
 366                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 367                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 368                                                         ifstream in2;
 369                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 370                                                         in2.close();
 371                                                         groupfileNames[i] = tryPath;
 372                                                 }
 373                                         }
 374
 375                                         in.close();
 376
 377                                         if (ableToOpen == 1) {
 378                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 379                                                 //erase from file list
 380                                                 groupfileNames.erase(groupfileNames.begin()+i);
 381                                                 i--;
 382                                         }else {
 383                                                 m->setGroupFile(groupfileNames[i]);
 384                                         }
 385                                 }
 386                         }
 387
 388                         if (groupfile != "") {
 389                                 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(); }
 390                         }else {
 391                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 392                         }
 393
 394                         //check for optional parameter and set defaults
 395                         // ...at some point should added some additional type checking...
 396                         string temp;
 397                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 398                         convert(temp, kmerSize);
 399
 400                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 401                         m->setProcessors(temp);
 402                         convert(temp, processors);
 403
 404                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 405
 406                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 407
 408                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 409                         convert(temp, match);
 410
 411                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 412                         convert(temp, misMatch);
 413
 414                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 415                         convert(temp, gapOpen);
 416
 417                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 418                         convert(temp, gapExtend);
 419
 420                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 421                         convert(temp, numWanted);
 422
 423                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 424                         convert(temp, cutoff);
 425
 426                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 427                         probs = m->isTrue(temp);
 428
 429                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 430                         convert(temp, iters);
 431
 432
 433
 434                         if ((method == "bayesian") && (search != "kmer"))  {
 435                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 436                                 search = "kmer";
 437                         }
 438                 }
 439
 440         }
 441         catch(exception& e) {
 442                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 443                 exit(1);
 444         }
 445 }
 446
 447 //**********************************************************************************************************************
 448 ClassifySeqsCommand::~ClassifySeqsCommand(){
 449         if (abort == false) {
 450                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 451         }
 452 }
 453 //**********************************************************************************************************************
 454
 455 int ClassifySeqsCommand::execute(){
 456         try {
 457                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 458
 459                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
 460                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
 461                 else {
 462                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 463                         m->mothurOutEndLine();
 464                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
 465                 }
 466
 467                 if (m->control_pressed) { delete classify; return 0; }
 468
 469
 470                 for (int s = 0; s < fastaFileNames.size(); s++) {
 471
 472                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 473
 474                         string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
 475                         RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
 476                         if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
 477                         RippedTaxName +=  ".";
 478
 479                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 480                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 481                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 482                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
 483
 484                         if ((method == "knn") && (search == "distance")) {
 485                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
 486                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 487                         }
 488
 489                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 490                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 491
 492                         int start = time(NULL);
 493                         int numFastaSeqs = 0;
 494                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 495
 496 #ifdef USE_MPI
 497                                 int pid, numSeqsPerProcessor;
 498                                 int tag = 2001;
 499                                 vector<unsigned long int> MPIPos;
 500
 501                                 MPI_Status status;
 502                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 503                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 504
 505                                 MPI_File inMPI;
 506                                 MPI_File outMPINewTax;
 507                                 MPI_File outMPITempTax;
 508
 509                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 510                                 int inMode=MPI_MODE_RDONLY;
 511
 512                                 char outNewTax[1024];
 513                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 514
 515                                 char outTempTax[1024];
 516                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 517
 518                                 char inFileName[1024];
 519                                 strcpy(inFileName, fastaFileNames[s].c_str());
 520
 521                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 522                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 523                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 524
 525                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 526
 527                                 if (pid == 0) { //you are the root process
 528
 529                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 530
 531                                         //send file positions to all processes
 532                                         for(int i = 1; i < processors; i++) {
 533                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 534                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 535                                         }
 536
 537                                         //figure out how many sequences you have to align
 538                                         numSeqsPerProcessor = numFastaSeqs / processors;
 539                                         int startIndex =  pid * numSeqsPerProcessor;
 540                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 541
 542
 543                                         //align your part
 544                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 545
 546                                         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;  }
 547
 548                                         for (int i = 1; i < processors; i++) {
 549                                                 int done;
 550                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 551                                         }
 552                                 }else{ //you are a child process
 553                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 554                                         MPIPos.resize(numFastaSeqs+1);
 555                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 556
 557                                         //figure out how many sequences you have to align
 558                                         numSeqsPerProcessor = numFastaSeqs / processors;
 559                                         int startIndex =  pid * numSeqsPerProcessor;
 560                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 561
 562
 563                                         //align your part
 564                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 565
 566                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 567
 568                                         int done = 0;
 569                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 570                                 }
 571
 572                                 //close files
 573                                 MPI_File_close(&inMPI);
 574                                 MPI_File_close(&outMPINewTax);
 575                                 MPI_File_close(&outMPITempTax);
 576                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 577
 578 #else
 579
 580                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 581
 582                         for (int i = 0; i < (positions.size()-1); i++) {
 583                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 584                         }
 585
 586                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 587                         if(processors == 1){
 588                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 589                         }
 590                         else{
 591                                 processIDS.resize(0);
 592
 593                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 594
 595                         }
 596         #else
 597                         numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 598         #endif
 599 #endif
 600
 601                 m->mothurOutEndLine();
 602                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 603                 start = time(NULL);
 604
 605
 606                 #ifdef USE_MPI
 607                         if (pid == 0) {  //this part does not need to be paralellized
 608
 609                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 610                 #else
 611                         //read namefile
 612                         if(namefile != "") {
 613
 614                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 615
 616                                 nameMap.clear(); //remove old names
 617
 618                                 ifstream inNames;
 619                                 m->openInputFile(namefileNames[s], inNames);
 620
 621                                 string firstCol, secondCol;
 622                                 while(!inNames.eof()) {
 623                                         inNames >> firstCol >> secondCol; m->gobble(inNames);
 624
 625                                         vector<string> temp;
 626                                         m->splitAtComma(secondCol, temp);
 627
 628                                         nameMap[firstCol] = temp;
 629                                 }
 630                                 inNames.close();
 631
 632                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 633                         }
 634                 #endif
 635
 636                         string group = "";
 637                         if (groupfile != "") {  group = groupfileNames[s]; }
 638
 639                         PhyloSummary taxaSum(taxonomyFileName, group);
 640
 641                         if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 642
 643                         if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
 644                         else {
 645                                 ifstream in;
 646                                 m->openInputFile(tempTaxonomyFile, in);
 647
 648                                 //read in users taxonomy file and add sequences to tree
 649                                 string name, taxon;
 650
 651                                 while(!in.eof()){
 652                                         in >> name >> taxon; m->gobble(in);
 653
 654                                         itNames = nameMap.find(name);
 655
 656                                         if (itNames == nameMap.end()) {
 657                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 658                                         }else{
 659                                                 for (int i = 0; i < itNames->second.size(); i++) {
 660                                                         taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 661                                                 }
 662                                                 itNames->second.clear();
 663                                                 nameMap.erase(itNames->first);
 664                                         }
 665                                 }
 666                                 in.close();
 667                         }
 668                         remove(tempTaxonomyFile.c_str());
 669
 670                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 671
 672                         //print summary file
 673                         ofstream outTaxTree;
 674                         m->openOutputFile(taxSummary, outTaxTree);
 675                         taxaSum.print(outTaxTree);
 676                         outTaxTree.close();
 677
 678                         //output taxonomy with the unclassified bins added
 679                         ifstream inTax;
 680                         m->openInputFile(newTaxonomyFile, inTax);
 681
 682                         ofstream outTax;
 683                         string unclass = newTaxonomyFile + ".unclass.temp";
 684                         m->openOutputFile(unclass, outTax);
 685
 686                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 687                         int maxLevel = taxaSum.getMaxLevel();
 688
 689                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 690                         string name, taxon;
 691                         while (!inTax.eof()) {
 692                                 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; }
 693
 694                                 inTax >> name >> taxon; m->gobble(inTax);
 695
 696                                 string newTax = addUnclassifieds(taxon, maxLevel);
 697
 698                                 outTax << name << '\t' << newTax << endl;
 699                         }
 700                         inTax.close();
 701                         outTax.close();
 702
 703                         remove(newTaxonomyFile.c_str());
 704                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 705
 706                         m->mothurOutEndLine();
 707                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 708
 709                         #ifdef USE_MPI
 710                                 }
 711                         #endif
 712
 713                         m->mothurOutEndLine();
 714                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 715                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 716                         m->mothurOutEndLine();
 717                 }
 718
 719                 //set taxonomy file as new current taxonomyfile
 720                 string current = "";
 721                 itTypes = outputTypes.find("taxonomy");
 722                 if (itTypes != outputTypes.end()) {
 723                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 724                 }
 725
 726                 delete classify;
 727                 return 0;
 728         }
 729         catch(exception& e) {
 730                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 731                 exit(1);
 732         }
 733 }
 734
 735 /**************************************************************************************************/
 736 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 737         try{
 738                 string newTax, taxon;
 739                 int level = 0;
 740
 741                 //keep what you have counting the levels
 742                 while (tax.find_first_of(';') != -1) {
 743                         //get taxon
 744                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 745                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 746                         newTax += taxon;
 747                         level++;
 748                 }
 749
 750                 //add "unclassified" until you reach maxLevel
 751                 while (level < maxlevel) {
 752                         newTax += "unclassified;";
 753                         level++;
 754                 }
 755
 756                 return newTax;
 757         }
 758         catch(exception& e) {
 759                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 760                 exit(1);
 761         }
 762 }
 763
 764 /**************************************************************************************************/
 765
 766 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
 767         try {
 768 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 769                 int process = 1;
 770                 int num = 0;
 771
 772                 //loop through and create all the processes you want
 773                 while (process != processors) {
 774                         int pid = fork();
 775
 776                         if (pid > 0) {
 777                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 778                                 process++;
 779                         }else if (pid == 0){
 780                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
 781
 782                                 //pass numSeqs to parent
 783                                 ofstream out;
 784                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 785                                 m->openOutputFile(tempFile, out);
 786                                 out << num << endl;
 787                                 out.close();
 788
 789                                 exit(0);
 790                         }else {
 791                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 792                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 793                                 exit(0);
 794                         }
 795                 }
 796
 797                 //parent does its part
 798                 num = driver(lines[0], taxFileName, tempTaxFile, filename);
 799
 800                 //force parent to wait until all the processes are done
 801                 for (int i=0;i<processIDS.size();i++) {
 802                         int temp = processIDS[i];
 803                         wait(&temp);
 804                 }
 805
 806                 for (int i = 0; i < processIDS.size(); i++) {
 807                         ifstream in;
 808                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 809                         m->openInputFile(tempFile, in);
 810                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 811                         in.close(); remove(tempFile.c_str());
 812                 }
 813
 814                 for(int i=0;i<processIDS.size();i++){
 815                         appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 816                         appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
 817                         remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
 818                         remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
 819                 }
 820
 821                 return num;
 822 #endif
 823         }
 824         catch(exception& e) {
 825                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 826                 exit(1);
 827         }
 828 }
 829 /**************************************************************************************************/
 830
 831 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
 832         try{
 833
 834                 ofstream output;
 835                 ifstream input;
 836                 m->openOutputFileAppend(filename, output);
 837                 m->openInputFile(temp, input);
 838
 839                 while(char c = input.get()){
 840                         if(input.eof())         {       break;                  }
 841                         else                            {       output << c;    }
 842                 }
 843
 844                 input.close();
 845                 output.close();
 846         }
 847         catch(exception& e) {
 848                 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
 849                 exit(1);
 850         }
 851 }
 852
 853 //**********************************************************************************************************************
 854
 855 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
 856         try {
 857                 ofstream outTax;
 858                 m->openOutputFile(taxFName, outTax);
 859
 860                 ofstream outTaxSimple;
 861                 m->openOutputFile(tempTFName, outTaxSimple);
 862
 863                 ifstream inFASTA;
 864                 m->openInputFile(filename, inFASTA);
 865
 866                 string taxonomy;
 867
 868                 inFASTA.seekg(filePos->start);
 869
 870                 bool done = false;
 871                 int count = 0;
 872
 873                 while (!done) {
 874                         if (m->control_pressed) { return 0; }
 875
 876                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
 877
 878                         if (candidateSeq->getName() != "") {
 879
 880                                 taxonomy = classify->getTaxonomy(candidateSeq);
 881
 882                                 if (m->control_pressed) { delete candidateSeq; return 0; }
 883
 884                                 if (taxonomy != "bad seq") {
 885                                         //output confidence scores or not
 886                                         if (probs) {
 887                                                 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
 888                                         }else{
 889                                                 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 890                                         }
 891
 892                                         outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 893                                 }
 894                                 count++;
 895                         }
 896                         delete candidateSeq;
 897
 898                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 899                                 unsigned long int pos = inFASTA.tellg();
 900                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 901                         #else
 902                                 if (inFASTA.eof()) { break; }
 903                         #endif
 904
 905                         //report progress
 906                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 907
 908                 }
 909                 //report progress
 910                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 911
 912                 inFASTA.close();
 913                 outTax.close();
 914                 outTaxSimple.close();
 915
 916                 return count;
 917         }
 918         catch(exception& e) {
 919                 m->errorOut(e, "ClassifySeqsCommand", "driver");
 920                 exit(1);
 921         }
 922 }
 923 //**********************************************************************************************************************
 924 #ifdef USE_MPI
 925 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
 926         try {
 927                 MPI_Status statusNew;
 928                 MPI_Status statusTemp;
 929                 MPI_Status status;
 930
 931                 int pid;
 932                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 933
 934                 string taxonomy;
 935                 string outputString;
 936
 937                 for(int i=0;i<num;i++){
 938
 939                         if (m->control_pressed) { return 0; }
 940
 941                         //read next sequence
 942                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 943                         char* buf4 = new char[length];
 944                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 945
 946                         string tempBuf = buf4;
 947                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 948                         istringstream iss (tempBuf,istringstream::in);
 949                         delete buf4;
 950
 951                         Sequence* candidateSeq = new Sequence(iss);
 952
 953                         if (candidateSeq->getName() != "") {
 954                                 taxonomy = classify->getTaxonomy(candidateSeq);
 955
 956                                 if (taxonomy != "bad seq") {
 957                                         //output confidence scores or not
 958                                         if (probs) {
 959                                                 outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
 960                                         }else{
 961                                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 962                                         }
 963
 964                                         int length = outputString.length();
 965                                         char* buf2 = new char[length];
 966                                         memcpy(buf2, outputString.c_str(), length);
 967
 968                                         MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
 969                                         delete buf2;
 970
 971                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 972                                         length = outputString.length();
 973                                         char* buf = new char[length];
 974                                         memcpy(buf, outputString.c_str(), length);
 975
 976                                         MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
 977                                         delete buf;
 978                                 }
 979                         }
 980                         delete candidateSeq;
 981
 982                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
 983                 }
 984
 985                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
 986
 987
 988                 return 1;
 989         }
 990         catch(exception& e) {
 991                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
 992                 exit(1);
 993         }
 994 }
 995
 996 //**********************************************************************************************************************
 997 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
 998         try {
 999
1000                 nameMap.clear(); //remove old names
1001
1002                 MPI_File inMPI;
1003                 MPI_Offset size;
1004                 MPI_Status status;
1005
1006                 //char* inFileName = new char[nameFilename.length()];
1007                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1008
1009                 char inFileName[1024];
1010                 strcpy(inFileName, nameFilename.c_str());
1011
1012                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1013                 MPI_File_get_size(inMPI, &size);
1014                 //delete inFileName;
1015
1016                 char* buffer = new char[size];
1017                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1018
1019                 string tempBuf = buffer;
1020                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
1021                 istringstream iss (tempBuf,istringstream::in);
1022                 delete buffer;
1023
1024                 string firstCol, secondCol;
1025                 while(!iss.eof()) {
1026                         iss >> firstCol >> secondCol; m->gobble(iss);
1027
1028                         vector<string> temp;
1029                         m->splitAtComma(secondCol, temp);
1030
1031                         nameMap[firstCol] = temp;
1032                 }
1033
1034                 MPI_File_close(&inMPI);
1035
1036                 return 1;
1037         }
1038         catch(exception& e) {
1039                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1040                 exit(1);
1041         }
1042 }
1043 #endif
1044 /**************************************************************************************************/