classifyseqscommand.cpp

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