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