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 pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  31                 CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
  32                 CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
  33                 CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
  34                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  35                 CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "ClassifySeqsCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string ClassifySeqsCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
  53                 helpString += "The classify.seqs command parameters are reference, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n";
  54                 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";
  55                 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";
  56                 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";
  57                 helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
  58                 helpString += "The method parameter allows you to specify classification method to use.  Your options are: bayesian and knn. The default is bayesian.\n";
  59                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n";
  60                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  61 #ifdef USE_MPI
  62                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  63 #endif
  64                 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.";
  65                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  66                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  67                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  68                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  69                 helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n";
  70                 helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n";
  71                 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";
  72                 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";
  73                 //helpString += "The flip parameter allows you shut off mothur's   The default is T.\n";
  74                 helpString += "The classify.seqs command should be in the following format: \n";
  75                 helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
  76                 helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
  77                 helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
  78                 helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
  79                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  80                 return helpString;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 ClassifySeqsCommand::ClassifySeqsCommand(){
  89         try {
  90                 abort = true; calledHelp = true;
  91                 setParameters();
  92                 vector<string> tempOutNames;
  93                 outputTypes["taxonomy"] = tempOutNames;
  94                 outputTypes["accnos"] = tempOutNames;
  95                 outputTypes["taxsummary"] = tempOutNames;
  96                 outputTypes["matchdist"] = tempOutNames;
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107                 rdb = ReferenceDB::getInstance();
 108
 109                 //allow user to run help
 110                 if(option == "help") { help(); abort = true; calledHelp = true; }
 111                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 112
 113                 else {
 114                         vector<string> myArray = setParameters();
 115
 116                         OptionParser parser(option);
 117                         map<string, string> parameters = parser.getParameters();
 118
 119                         ValidParameters validParameter("classify.seqs");
 120                         map<string, string>::iterator it;
 121
 122                         //check to make sure all parameters are valid for command
 123                         for (it = parameters.begin(); it != parameters.end(); it++) {
 124                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 125                         }
 126
 127                         //initialize outputTypes
 128                         vector<string> tempOutNames;
 129                         outputTypes["taxonomy"] = tempOutNames;
 130                         outputTypes["taxsummary"] = tempOutNames;
 131                         outputTypes["matchdist"] = tempOutNames;
 132                         outputTypes["accnos"] = tempOutNames;
 133
 134                         //if the user changes the output directory command factory will send this info to us in the output parameter
 135                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 136
 137                         //if the user changes the input directory command factory will send this info to us in the output parameter
 138                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 139                         if (inputDir == "not found"){   inputDir = "";          }
 140                         else {
 141                                 string path;
 142                                 it = parameters.find("reference");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 148                                 }
 149
 150                                 it = parameters.find("taxonomy");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 156                                 }
 157
 158                                 it = parameters.find("group");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 164                                 }
 165                         }
 166
 167                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 168                         if (fastaFileName == "not found") {
 169                                 //if there is a current fasta file, use it
 170                                 string filename = m->getFastaFile();
 171                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 172                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 173                         }
 174                         else {
 175                                 m->splitAtDash(fastaFileName, fastaFileNames);
 176
 177                                 //go through files and make sure they are good, if not, then disregard them
 178                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 179
 180                                         bool ignore = false;
 181                                         if (fastaFileNames[i] == "current") {
 182                                                 fastaFileNames[i] = m->getFastaFile();
 183                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 184                                                 else {
 185                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 186                                                         //erase from file list
 187                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 188                                                         i--;
 189                                                 }
 190                                         }
 191
 192                                         if (!ignore) {
 193
 194                                                 if (inputDir != "") {
 195                                                         string path = m->hasPath(fastaFileNames[i]);
 196                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 197                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 198                                                 }
 199
 200                                                 int ableToOpen;
 201
 202                                                 ifstream in;
 203                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 204
 205                                                 //if you can't open it, try default location
 206                                                 if (ableToOpen == 1) {
 207                                                         if (m->getDefaultPath() != "") { //default path is set
 208                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 209                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 210                                                                 ifstream in2;
 211                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 212                                                                 in2.close();
 213                                                                 fastaFileNames[i] = tryPath;
 214                                                         }
 215                                                 }
 216
 217                                                 if (ableToOpen == 1) {
 218                                                         if (m->getOutputDir() != "") { //default path is set
 219                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 220                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 221                                                                 ifstream in2;
 222                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 223                                                                 in2.close();
 224                                                                 fastaFileNames[i] = tryPath;
 225                                                         }
 226                                                 }
 227
 228                                                 in.close();
 229
 230                                                 if (ableToOpen == 1) {
 231                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 232                                                         //erase from file list
 233                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 234                                                         i--;
 235                                                 }else {
 236                                                         m->setFastaFile(fastaFileNames[i]);
 237                                                 }
 238                                         }
 239
 240                                 }
 241
 242                                 //make sure there is at least one valid file left
 243                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 244                         }
 245
 246                         namefile = validParameter.validFile(parameters, "name", false);
 247                         if (namefile == "not found") { namefile = "";  }
 248
 249                         else {
 250                                 m->splitAtDash(namefile, namefileNames);
 251
 252                                 //go through files and make sure they are good, if not, then disregard them
 253                                 for (int i = 0; i < namefileNames.size(); i++) {
 254                                         bool ignore = false;
 255                                         if (namefileNames[i] == "current") {
 256                                                 namefileNames[i] = m->getNameFile();
 257                                                 if (namefileNames[i] != "") {  m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 258                                                 else {
 259                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 260                                                         //erase from file list
 261                                                         namefileNames.erase(namefileNames.begin()+i);
 262                                                         i--;
 263                                                 }
 264                                         }
 265
 266                                         if (!ignore) {
 267
 268                                                 if (inputDir != "") {
 269                                                         string path = m->hasPath(namefileNames[i]);
 270                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 271                                                         if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 272                                                 }
 273                                                 int ableToOpen;
 274
 275                                                 ifstream in;
 276                                                 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 277
 278                                                 //if you can't open it, try default location
 279                                                 if (ableToOpen == 1) {
 280                                                         if (m->getDefaultPath() != "") { //default path is set
 281                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 282                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 283                                                                 ifstream in2;
 284                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 285                                                                 in2.close();
 286                                                                 namefileNames[i] = tryPath;
 287                                                         }
 288                                                 }
 289
 290                                                 if (ableToOpen == 1) {
 291                                                         if (m->getOutputDir() != "") { //default path is set
 292                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 293                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 294                                                                 ifstream in2;
 295                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 296                                                                 in2.close();
 297                                                                 namefileNames[i] = tryPath;
 298                                                         }
 299                                                 }
 300                                                 in.close();
 301
 302                                                 if (ableToOpen == 1) {
 303                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 304                                                         //erase from file list
 305                                                         namefileNames.erase(namefileNames.begin()+i);
 306                                                         i--;
 307                                                 }else {
 308                                                         m->setNameFile(namefileNames[i]);
 309                                                 }
 310                                         }
 311                                 }
 312                         }
 313
 314                         if (namefile != "") {
 315                                 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(); }
 316                         }
 317
 318                         groupfile = validParameter.validFile(parameters, "group", false);
 319                         if (groupfile == "not found") { groupfile = "";  }
 320                         else {
 321                                 m->splitAtDash(groupfile, groupfileNames);
 322
 323                                 //go through files and make sure they are good, if not, then disregard them
 324                                 for (int i = 0; i < groupfileNames.size(); i++) {
 325                                         if (inputDir != "") {
 326                                                 string path = m->hasPath(groupfileNames[i]);
 327                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 328                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 329                                         }
 330                                         int ableToOpen;
 331
 332                                         ifstream in;
 333                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 334
 335                                         //if you can't open it, try default location
 336                                         if (ableToOpen == 1) {
 337                                                 if (m->getDefaultPath() != "") { //default path is set
 338                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 339                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 340                                                         ifstream in2;
 341                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 342                                                         in2.close();
 343                                                         groupfileNames[i] = tryPath;
 344                                                 }
 345                                         }
 346
 347                                         if (ableToOpen == 1) {
 348                                                 if (m->getOutputDir() != "") { //default path is set
 349                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 350                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 351                                                         ifstream in2;
 352                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 353                                                         in2.close();
 354                                                         groupfileNames[i] = tryPath;
 355                                                 }
 356                                         }
 357
 358                                         in.close();
 359
 360                                         if (ableToOpen == 1) {
 361                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 362                                                 //erase from file list
 363                                                 groupfileNames.erase(groupfileNames.begin()+i);
 364                                                 i--;
 365                                         }else {
 366                                                 m->setGroupFile(groupfileNames[i]);
 367                                         }
 368                                 }
 369                         }
 370
 371                         if (groupfile != "") {
 372                                 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(); }
 373                         }else {
 374                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 375                         }
 376
 377                         //check for optional parameter and set defaults
 378                         // ...at some point should added some additional type checking...
 379                         string temp;
 380                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 381                         m->mothurConvert(temp, kmerSize);
 382
 383                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 384                         m->setProcessors(temp);
 385                         m->mothurConvert(temp, processors);
 386
 387                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 388                         save = m->isTrue(temp);
 389                         rdb->save = save;
 390                         if (save) { //clear out old references
 391                                 rdb->clearMemory();
 392                         }
 393
 394                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 395                         templateFileName = validParameter.validFile(parameters, "reference", true);
 396                         if (templateFileName == "not found") {
 397                                 //check for saved reference sequences
 398                                 if (rdb->referenceSeqs.size() != 0) {
 399                                         templateFileName = "saved";
 400                                 }else {
 401                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the classify.seqs command.");
 402                                         m->mothurOutEndLine();
 403                                         abort = true;
 404                                 }
 405                         }else if (templateFileName == "not open") { abort = true; }
 406                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 407
 408                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 409                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 410                         if (taxonomyFileName == "not found") {
 411                                 //check for saved reference sequences
 412                                 if (rdb->wordGenusProb.size() != 0) {
 413                                         taxonomyFileName = "saved";
 414                                 }else {
 415                                         m->mothurOut("[ERROR]: You don't have any saved taxonomy information and the taxonomy parameter is a required for the classify.seqs command.");
 416                                         m->mothurOutEndLine();
 417                                         abort = true;
 418                                 }
 419                         }else if (taxonomyFileName == "not open") { abort = true; }
 420                         else {  if (save) {     rdb->setSavedTaxonomy(taxonomyFileName);        }       }
 421
 422                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 423
 424                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 425
 426                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 427                         m->mothurConvert(temp, match);
 428
 429                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 430                         m->mothurConvert(temp, misMatch);
 431
 432                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 433                         m->mothurConvert(temp, gapOpen);
 434
 435                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 436                         m->mothurConvert(temp, gapExtend);
 437
 438                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 439                         m->mothurConvert(temp, numWanted);
 440
 441                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 442                         m->mothurConvert(temp, cutoff);
 443
 444                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 445                         probs = m->isTrue(temp);
 446
 447                         //temp = validParameter.validFile(parameters, "flip", false);                   if (temp == "not found"){       temp = "T";                             }
 448                         //flip = m->isTrue(temp);
 449                         flip = true;
 450
 451                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 452                         m->mothurConvert(temp, iters);
 453
 454
 455                         if ((method == "bayesian") && (search != "kmer"))  {
 456                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 457                                 search = "kmer";
 458                         }
 459
 460             if (!abort) {
 461                 if (namefileNames.size() == 0){
 462                     if (fastaFileNames.size() != 0) {
 463                         vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
 464                         parser.getNameFile(files);
 465                     }
 466                 }
 467             }
 468
 469                 }
 470         }
 471         catch(exception& e) {
 472                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 473                 exit(1);
 474         }
 475 }
 476
 477 //**********************************************************************************************************************
 478 ClassifySeqsCommand::~ClassifySeqsCommand(){
 479         if (abort == false) {
 480                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 481         }
 482 }
 483 //**********************************************************************************************************************
 484
 485 int ClassifySeqsCommand::execute(){
 486         try {
 487                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 488
 489                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);             }
 490                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
 491                 else {
 492                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 493                         m->mothurOutEndLine();
 494                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);
 495                 }
 496
 497                 if (m->control_pressed) { delete classify; return 0; }
 498
 499                 for (int s = 0; s < fastaFileNames.size(); s++) {
 500
 501                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 502
 503                         string baseTName = taxonomyFileName;
 504                         if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy();  }
 505
 506                         string RippedTaxName = m->getRootName(m->getSimpleName(baseTName));
 507                         RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
 508                         if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
 509                         if (RippedTaxName != "") { RippedTaxName +=  "."; }
 510
 511                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 512                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 513                         string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "flip.accnos";
 514                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 515                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
 516
 517                         if ((method == "knn") && (search == "distance")) {
 518                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
 519                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 520                         }
 521
 522                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 523                         outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
 524                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 525
 526                         int start = time(NULL);
 527                         int numFastaSeqs = 0;
 528                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 529
 530 #ifdef USE_MPI
 531                                 int pid, numSeqsPerProcessor;
 532                                 int tag = 2001;
 533                                 vector<unsigned long long> MPIPos;
 534
 535                                 MPI_Status status;
 536                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 537                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 538
 539                                 MPI_File inMPI;
 540                                 MPI_File outMPINewTax;
 541                                 MPI_File outMPITempTax;
 542                                 MPI_File outMPIAcc;
 543
 544                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 545                                 int inMode=MPI_MODE_RDONLY;
 546
 547                                 char outNewTax[1024];
 548                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 549
 550                                 char outTempTax[1024];
 551                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 552
 553                                 char outAcc[1024];
 554                                 strcpy(outAcc, newaccnosFile.c_str());
 555
 556                                 char inFileName[1024];
 557                                 strcpy(inFileName, fastaFileNames[s].c_str());
 558
 559                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 560                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 561                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 562                                 MPI_File_open(MPI_COMM_WORLD, outAcc, outMode, MPI_INFO_NULL, &outMPIAcc);
 563
 564                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);  MPI_File_close(&outMPIAcc);   MPI_File_close(&outMPITempTax);  delete classify;  return 0;  }
 565
 566                                 if (pid == 0) { //you are the root process
 567
 568                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 569
 570                                         //send file positions to all processes
 571                                         for(int i = 1; i < processors; i++) {
 572                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 573                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 574                                         }
 575
 576                                         //figure out how many sequences you have to align
 577                                         numSeqsPerProcessor = numFastaSeqs / processors;
 578                                         int startIndex =  pid * numSeqsPerProcessor;
 579                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 580
 581
 582                                         //align your part
 583                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 584
 585                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc);   MPI_File_close(&outMPITempTax);  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } delete classify; return 0;  }
 586
 587                                         for (int i = 1; i < processors; i++) {
 588                                                 int done;
 589                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 590                                         }
 591                                 }else{ //you are a child process
 592                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 593                                         MPIPos.resize(numFastaSeqs+1);
 594                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 595
 596                                         //figure out how many sequences you have to align
 597                                         numSeqsPerProcessor = numFastaSeqs / processors;
 598                                         int startIndex =  pid * numSeqsPerProcessor;
 599                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 600
 601
 602                                         //align your part
 603                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 604
 605                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);  MPI_File_close(&outMPIAcc);  MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 606
 607                                         int done = 0;
 608                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 609                                 }
 610
 611                                 //close files
 612                                 MPI_File_close(&inMPI);
 613                                 MPI_File_close(&outMPINewTax);
 614                                 MPI_File_close(&outMPITempTax);
 615                                 MPI_File_close(&outMPIAcc);
 616                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 617
 618 #else
 619
 620                         vector<unsigned long long> positions;
 621 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 622                         positions = m->divideFile(fastaFileNames[s], processors);
 623                         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 624 #else
 625                         if (processors == 1) {
 626                                 lines.push_back(new linePair(0, 1000));
 627                         }else {
 628                                 positions = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs);
 629                 if (positions.size() < processors) { processors = positions.size(); }
 630
 631                                 //figure out how many sequences you have to process
 632                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 633                                 for (int i = 0; i < processors; i++) {
 634                                         int startIndex =  i * numSeqsPerProcessor;
 635                                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 636                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 637                                 }
 638                         }
 639 #endif
 640                         if(processors == 1){
 641                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 642                         }else{
 643                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 644                         }
 645 #endif
 646
 647                         if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); }
 648
 649                 m->mothurOutEndLine();
 650                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 651                 start = time(NULL);
 652
 653
 654
 655                 #ifdef USE_MPI
 656                         if (pid == 0) {  //this part does not need to be paralellized
 657
 658                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 659                 #else
 660                         //read namefile
 661                         if(namefile != "") {
 662
 663                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 664
 665                                 nameMap.clear(); //remove old names
 666
 667                                 ifstream inNames;
 668                                 m->openInputFile(namefileNames[s], inNames);
 669
 670                                 string firstCol, secondCol;
 671                                 while(!inNames.eof()) {
 672                                         inNames >> firstCol >> secondCol; m->gobble(inNames);
 673
 674                                         vector<string> temp;
 675                                         m->splitAtComma(secondCol, temp);
 676
 677                                         nameMap[firstCol] = temp;
 678                                 }
 679                                 inNames.close();
 680
 681                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 682                         }
 683                 #endif
 684
 685                         string group = "";
 686                         if (groupfile != "") {  group = groupfileNames[s]; }
 687
 688                         PhyloSummary taxaSum(baseTName, group);
 689
 690                         if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 691
 692                         if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
 693                         else {
 694                                 ifstream in;
 695                                 m->openInputFile(tempTaxonomyFile, in);
 696
 697                                 //read in users taxonomy file and add sequences to tree
 698                                 string name, taxon;
 699
 700                                 while(!in.eof()){
 701                                         in >> name >> taxon; m->gobble(in);
 702
 703                                         itNames = nameMap.find(name);
 704
 705                                         if (itNames == nameMap.end()) {
 706                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 707                                         }else{
 708                                                 for (int i = 0; i < itNames->second.size(); i++) {
 709                                                         taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 710                                                 }
 711                                                 itNames->second.clear();
 712                                                 nameMap.erase(itNames->first);
 713                                         }
 714                                 }
 715                                 in.close();
 716                         }
 717                         m->mothurRemove(tempTaxonomyFile);
 718
 719                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 720
 721                         //print summary file
 722                         ofstream outTaxTree;
 723                         m->openOutputFile(taxSummary, outTaxTree);
 724                         taxaSum.print(outTaxTree);
 725                         outTaxTree.close();
 726
 727                         //output taxonomy with the unclassified bins added
 728                         ifstream inTax;
 729                         m->openInputFile(newTaxonomyFile, inTax);
 730
 731                         ofstream outTax;
 732                         string unclass = newTaxonomyFile + ".unclass.temp";
 733                         m->openOutputFile(unclass, outTax);
 734
 735                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 736                         int maxLevel = taxaSum.getMaxLevel();
 737
 738                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 739                         string name, taxon;
 740                         while (!inTax.eof()) {
 741                                 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; }
 742
 743                                 inTax >> name >> taxon; m->gobble(inTax);
 744
 745                                 string newTax = addUnclassifieds(taxon, maxLevel);
 746
 747                                 outTax << name << '\t' << newTax << endl;
 748                         }
 749                         inTax.close();
 750                         outTax.close();
 751
 752                         m->mothurRemove(newTaxonomyFile);
 753                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 754
 755                         m->mothurOutEndLine();
 756                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 757
 758                         #ifdef USE_MPI
 759                                 }
 760                         #endif
 761
 762                         m->mothurOutEndLine();
 763                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 764                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 765                         m->mothurOutEndLine();
 766                 }
 767
 768                 //set taxonomy file as new current taxonomyfile
 769                 string current = "";
 770                 itTypes = outputTypes.find("taxonomy");
 771                 if (itTypes != outputTypes.end()) {
 772                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 773                 }
 774
 775                 current = "";
 776                 itTypes = outputTypes.find("accnos");
 777                 if (itTypes != outputTypes.end()) {
 778                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 779                 }
 780
 781                 delete classify;
 782
 783                 return 0;
 784         }
 785         catch(exception& e) {
 786                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 787                 exit(1);
 788         }
 789 }
 790
 791 /**************************************************************************************************/
 792 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 793         try{
 794                 string newTax, taxon;
 795                 int level = 0;
 796
 797                 //keep what you have counting the levels
 798                 while (tax.find_first_of(';') != -1) {
 799                         //get taxon
 800                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 801                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 802                         newTax += taxon;
 803                         level++;
 804                 }
 805
 806                 //add "unclassified" until you reach maxLevel
 807                 while (level < maxlevel) {
 808                         newTax += "unclassified;";
 809                         level++;
 810                 }
 811
 812                 return newTax;
 813         }
 814         catch(exception& e) {
 815                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 816                 exit(1);
 817         }
 818 }
 819
 820 /**************************************************************************************************/
 821
 822 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
 823         try {
 824
 825                 int num = 0;
 826                 processIDS.clear();
 827
 828 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 829                 int process = 1;
 830
 831                 //loop through and create all the processes you want
 832                 while (process != processors) {
 833                         int pid = fork();
 834
 835                         if (pid > 0) {
 836                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 837                                 process++;
 838                         }else if (pid == 0){
 839                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", filename);
 840
 841                                 //pass numSeqs to parent
 842                                 ofstream out;
 843                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 844                                 m->openOutputFile(tempFile, out);
 845                                 out << num << endl;
 846                                 out.close();
 847
 848                                 exit(0);
 849                         }else {
 850                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 851                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 852                                 exit(0);
 853                         }
 854                 }
 855
 856                 //parent does its part
 857                 num = driver(lines[0], taxFileName, tempTaxFile, accnos, filename);
 858
 859                 //force parent to wait until all the processes are done
 860                 for (int i=0;i<processIDS.size();i++) {
 861                         int temp = processIDS[i];
 862                         wait(&temp);
 863                 }
 864
 865                 for (int i = 0; i < processIDS.size(); i++) {
 866                         ifstream in;
 867                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 868                         m->openInputFile(tempFile, in);
 869                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 870                         in.close(); m->mothurRemove(m->getFullPathName(tempFile));
 871                 }
 872 #else
 873                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 874                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
 875                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 876                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 877
 878                 vector<classifyData*> pDataArray;
 879                 DWORD   dwThreadIdArray[processors-1];
 880                 HANDLE  hThreadArray[processors-1];
 881
 882                 //Create processor worker threads.
 883                 for( int i=0; i<processors-1; i++ ){
 884                         // Allocate memory for thread data.
 885                         string extension = "";
 886                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 887
 888                         classifyData* tempclass = new classifyData((accnos + extension), 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, flip);
 889                         pDataArray.push_back(tempclass);
 890
 891                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 892                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 893                         hThreadArray[i] = CreateThread(NULL, 0, MyClassThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 894
 895                 }
 896
 897                 //parent does its part
 898                 num = driver(lines[processors-1], taxFileName + toString(processors-1) + ".temp", tempTaxFile + toString(processors-1) + ".temp", accnos + toString(processors-1) + ".temp", filename);
 899                 processIDS.push_back((processors-1));
 900
 901                 //Wait until all threads have terminated.
 902                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 903
 904                 //Close all thread handles and free memory allocations.
 905                 for(int i=0; i < pDataArray.size(); i++){
 906                         num += pDataArray[i]->count;
 907                         CloseHandle(hThreadArray[i]);
 908                         delete pDataArray[i];
 909                 }
 910
 911         #endif
 912         vector<string> nonBlankAccnosFiles;
 913                 if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
 914                 else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
 915
 916                 for(int i=0;i<processIDS.size();i++){
 917                         appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 918                         appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
 919             if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
 920                                 nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
 921                         }else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
 922
 923                         m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
 924                         m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
 925                 }
 926
 927         //append accnos files
 928                 if (nonBlankAccnosFiles.size() != 0) {
 929                         rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
 930
 931                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 932                                 appendTaxFiles(nonBlankAccnosFiles[h], accnos);
 933                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 934                         }
 935                 }else { //recreate the accnosfile if needed
 936                         ofstream out;
 937                         m->openOutputFile(accnos, out);
 938                         out.close();
 939                 }
 940
 941                 return num;
 942
 943         }
 944         catch(exception& e) {
 945                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 946                 exit(1);
 947         }
 948 }
 949 /**************************************************************************************************/
 950
 951 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
 952         try{
 953
 954                 ofstream output;
 955                 ifstream input;
 956                 m->openOutputFileAppend(filename, output);
 957                 m->openInputFile(temp, input);
 958
 959                 while(char c = input.get()){
 960                         if(input.eof())         {       break;                  }
 961                         else                            {       output << c;    }
 962                 }
 963
 964                 input.close();
 965                 output.close();
 966         }
 967         catch(exception& e) {
 968                 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
 969                 exit(1);
 970         }
 971 }
 972
 973 //**********************************************************************************************************************
 974
 975 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
 976         try {
 977                 ofstream outTax;
 978                 m->openOutputFile(taxFName, outTax);
 979
 980                 ofstream outTaxSimple;
 981                 m->openOutputFile(tempTFName, outTaxSimple);
 982
 983                 ofstream outAcc;
 984                 m->openOutputFile(accnos, outAcc);
 985
 986                 ifstream inFASTA;
 987                 m->openInputFile(filename, inFASTA);
 988
 989                 string taxonomy;
 990
 991                 inFASTA.seekg(filePos->start);
 992
 993                 bool done = false;
 994                 int count = 0;
 995
 996                 while (!done) {
 997                         if (m->control_pressed) {
 998                                 inFASTA.close();
 999                                 outTax.close();
1000                                 outTaxSimple.close();
1001                                 outAcc.close(); return 0; }
1002
1003                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
1004
1005                         if (candidateSeq->getName() != "") {
1006
1007                                 taxonomy = classify->getTaxonomy(candidateSeq);
1008
1009                                 if (m->control_pressed) { delete candidateSeq; return 0; }
1010
1011                                 if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
1012
1013                                 //output confidence scores or not
1014                                 if (probs) {
1015                                         outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
1016                                 }else{
1017                                         outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1018                                 }
1019
1020                                 if (classify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
1021
1022                                 outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1023
1024                                 count++;
1025                         }
1026                         delete candidateSeq;
1027
1028                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1029                                 unsigned long long pos = inFASTA.tellg();
1030                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1031                         #else
1032                                 if (inFASTA.eof()) { break; }
1033                         #endif
1034
1035                         //report progress
1036                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1037
1038                 }
1039                 //report progress
1040                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1041
1042                 inFASTA.close();
1043                 outTax.close();
1044                 outTaxSimple.close();
1045                 outAcc.close();
1046
1047                 return count;
1048         }
1049         catch(exception& e) {
1050                 m->errorOut(e, "ClassifySeqsCommand", "driver");
1051                 exit(1);
1052         }
1053 }
1054 //**********************************************************************************************************************
1055 #ifdef USE_MPI
1056 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, MPI_File& accFile, vector<unsigned long long>& MPIPos){
1057         try {
1058                 MPI_Status statusNew;
1059                 MPI_Status statusTemp;
1060                 MPI_Status statusAcc;
1061                 MPI_Status status;
1062
1063                 int pid;
1064                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1065
1066                 string taxonomy;
1067                 string outputString;
1068
1069                 for(int i=0;i<num;i++){
1070
1071                         if (m->control_pressed) { return 0; }
1072
1073                         //read next sequence
1074                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1075                         char* buf4 = new char[length];
1076                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1077
1078                         string tempBuf = buf4;
1079                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1080                         istringstream iss (tempBuf,istringstream::in);
1081                         delete buf4;
1082
1083                         Sequence* candidateSeq = new Sequence(iss);
1084
1085                         if (candidateSeq->getName() != "") {
1086                                 taxonomy = classify->getTaxonomy(candidateSeq);
1087
1088                                 if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
1089
1090                                 //output confidence scores or not
1091                                 if (probs) {
1092                                         outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
1093                                 }else{
1094                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1095                                 }
1096
1097                                 int length = outputString.length();
1098                                 char* buf2 = new char[length];
1099                                 memcpy(buf2, outputString.c_str(), length);
1100
1101                                 MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
1102                                 delete buf2;
1103
1104                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1105                                 length = outputString.length();
1106                                 char* buf = new char[length];
1107                                 memcpy(buf, outputString.c_str(), length);
1108
1109                                 MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
1110                                 delete buf;
1111
1112                                 if (classify->getFlipped()) {
1113                                         outputString =  candidateSeq->getName() + "\n";
1114                                         length = outputString.length();
1115                                         char* buf3 = new char[length];
1116                                         memcpy(buf3, outputString.c_str(), length);
1117
1118                                         MPI_File_write_shared(accFile, buf3, length, MPI_CHAR, &statusAcc);
1119                                         delete buf3;
1120                                 }
1121
1122                         }
1123                         delete candidateSeq;
1124
1125                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
1126                 }
1127
1128                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
1129
1130
1131                 return 1;
1132         }
1133         catch(exception& e) {
1134                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
1135                 exit(1);
1136         }
1137 }
1138
1139 //**********************************************************************************************************************
1140 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
1141         try {
1142
1143                 nameMap.clear(); //remove old names
1144
1145                 MPI_File inMPI;
1146                 MPI_Offset size;
1147                 MPI_Status status;
1148
1149                 //char* inFileName = new char[nameFilename.length()];
1150                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1151
1152                 char inFileName[1024];
1153                 strcpy(inFileName, nameFilename.c_str());
1154
1155                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1156                 MPI_File_get_size(inMPI, &size);
1157                 //delete inFileName;
1158
1159                 char* buffer = new char[size];
1160                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1161
1162                 string tempBuf = buffer;
1163                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
1164                 istringstream iss (tempBuf,istringstream::in);
1165                 delete buffer;
1166
1167                 string firstCol, secondCol;
1168                 while(!iss.eof()) {
1169                         iss >> firstCol >> secondCol; m->gobble(iss);
1170
1171                         vector<string> temp;
1172                         m->splitAtComma(secondCol, temp);
1173
1174                         nameMap[firstCol] = temp;
1175                 }
1176
1177                 MPI_File_close(&inMPI);
1178
1179                 return 1;
1180         }
1181         catch(exception& e) {
1182                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1183                 exit(1);
1184         }
1185 }
1186 #endif
1187 /**************************************************************************************************/