classifyseqscommand.cpp

   1 /*
   2  *  classifyseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/2/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "classifyseqscommand.h"
  11 #include "sequence.hpp"
  12 #include "bayesian.h"
  13 #include "phylotree.h"
  14 #include "knn.h"
  15
  16 //**********************************************************************************************************************
  17
  18 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
  19         try {
  20                 abort = false;
  21
  22                 //allow user to run help
  23                 if(option == "help") { help(); abort = true; }
  24
  25                 else {
  26
  27                         //valid paramters for this command
  28                         string AlignArray[] =  {"template","fasta","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
  29                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  30
  31                         OptionParser parser(option);
  32                         map<string, string> parameters = parser.getParameters();
  33
  34                         ValidParameters validParameter;
  35                         map<string, string>::iterator it;
  36
  37                         //check to make sure all parameters are valid for command
  38                         for (it = parameters.begin(); it != parameters.end(); it++) {
  39                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  40                         }
  41
  42                         //if the user changes the output directory command factory will send this info to us in the output parameter
  43                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  44
  45                         //if the user changes the input directory command factory will send this info to us in the output parameter
  46                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  47                         if (inputDir == "not found"){   inputDir = "";          }
  48                         else {
  49                                 string path;
  50                                 it = parameters.find("template");
  51                                 //user has given a template file
  52                                 if(it != parameters.end()){
  53                                         path = hasPath(it->second);
  54                                         //if the user has not given a path then, add inputdir. else leave path alone.
  55                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  56                                 }
  57
  58                                 it = parameters.find("taxonomy");
  59                                 //user has given a template file
  60                                 if(it != parameters.end()){
  61                                         path = hasPath(it->second);
  62                                         //if the user has not given a path then, add inputdir. else leave path alone.
  63                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
  64                                 }
  65                         }
  66
  67                         //check for required parameters
  68                         templateFileName = validParameter.validFile(parameters, "template", true);
  69                         if (templateFileName == "not found") {
  70                                 m->mothurOut("template is a required parameter for the classify.seqs command.");
  71                                 m->mothurOutEndLine();
  72                                 abort = true;
  73                         }
  74                         else if (templateFileName == "not open") { abort = true; }
  75
  76                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
  77                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true;  }
  78                         else {
  79                                 splitAtDash(fastaFileName, fastaFileNames);
  80
  81                                 //go through files and make sure they are good, if not, then disregard them
  82                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  83                                         if (inputDir != "") {
  84                                                 string path = hasPath(fastaFileNames[i]);
  85                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  86                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  87                                         }
  88
  89                                         int ableToOpen;
  90                                         ifstream in;
  91                                         ableToOpen = openInputFile(fastaFileNames[i], in);
  92                                         if (ableToOpen == 1) {
  93                                                 m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  94                                                 //erase from file list
  95                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
  96                                                 i--;
  97                                         }
  98                                         in.close();
  99                                 }
 100
 101                                 //make sure there is at least one valid file left
 102                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 103                         }
 104
 105
 106                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 107                         if (taxonomyFileName == "not found") {
 108                                 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
 109                                 m->mothurOutEndLine();
 110                                 abort = true;
 111                         }
 112                         else if (taxonomyFileName == "not open") { abort = true; }
 113
 114
 115                         namefile = validParameter.validFile(parameters, "name", false);
 116                         if (namefile == "not found") { namefile = "";  }
 117
 118                         else {
 119                                 splitAtDash(namefile, namefileNames);
 120
 121                                 //go through files and make sure they are good, if not, then disregard them
 122                                 for (int i = 0; i < namefileNames.size(); i++) {
 123                                         if (inputDir != "") {
 124                                                 string path = hasPath(namefileNames[i]);
 125                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 126                                                 if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 127                                         }
 128
 129                                         int ableToOpen;
 130                                         ifstream in;
 131                                         ableToOpen = openInputFile(namefileNames[i], in);
 132                                         if (ableToOpen == 1) {  m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true;        }
 133                                         in.close();
 134                                 }
 135                         }
 136
 137                         if (namefile != "") {
 138                                 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(); }
 139                         }
 140
 141                         //check for optional parameter and set defaults
 142                         // ...at some point should added some additional type checking...
 143                         string temp;
 144                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 145                         convert(temp, kmerSize);
 146
 147                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 148                         convert(temp, processors);
 149
 150                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 151
 152                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 153
 154                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 155                         convert(temp, match);
 156
 157                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 158                         convert(temp, misMatch);
 159
 160                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 161                         convert(temp, gapOpen);
 162
 163                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 164                         convert(temp, gapExtend);
 165
 166                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 167                         convert(temp, numWanted);
 168
 169                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 170                         convert(temp, cutoff);
 171
 172                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 173                         probs = isTrue(temp);
 174
 175                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 176                         convert(temp, iters);
 177
 178
 179
 180                         if ((method == "bayesian") && (search != "kmer"))  {
 181                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 182                                 search = "kmer";
 183                         }
 184                 }
 185
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 189                 exit(1);
 190         }
 191 }
 192
 193 //**********************************************************************************************************************
 194
 195 ClassifySeqsCommand::~ClassifySeqsCommand(){
 196
 197         if (abort == false) {
 198                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 199         }
 200 }
 201
 202 //**********************************************************************************************************************
 203
 204 void ClassifySeqsCommand::help(){
 205         try {
 206                 m->mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n");
 207                 m->mothurOut("The classify.seqs command parameters are template, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
 208                 m->mothurOut("The template, 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");
 209                 m->mothurOut("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");
 210                 m->mothurOut("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");
 211                 m->mothurOut("The method parameter allows you to specify classification method to use.  Your options are: bayesian and knn. The default is bayesian.\n");
 212                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 213                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 214                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 215                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 216                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 217                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 218                 m->mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n");
 219                 m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n");
 220                 m->mothurOut("The probs parameter shut off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be run.\n");
 221                 m->mothurOut("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");
 222                 m->mothurOut("The classify.seqs command should be in the following format: \n");
 223                 m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
 224                 m->mothurOut("Example classify.seqs(fasta=amazon.fasta, template=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n");
 225                 m->mothurOut("The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n");
 226                 m->mothurOut("The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n");
 227                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "ClassifySeqsCommand", "help");
 231                 exit(1);
 232         }
 233 }
 234
 235
 236 //**********************************************************************************************************************
 237
 238 int ClassifySeqsCommand::execute(){
 239         try {
 240                 if (abort == true) {    return 0;       }
 241
 242                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
 243                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
 244                 else {
 245                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 246                         m->mothurOutEndLine();
 247                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
 248                 }
 249
 250                 if (m->control_pressed) { delete classify; return 0; }
 251
 252                 vector<string> outputNames;
 253
 254                 for (int s = 0; s < fastaFileNames.size(); s++) {
 255
 256                         //read namefile
 257                         if(namefile != "") {
 258                                 nameMap.clear(); //remove old names
 259
 260                                 ifstream inNames;
 261                                 openInputFile(namefileNames[s], inNames);
 262
 263                                 string firstCol, secondCol;
 264                                 while(!inNames.eof()) {
 265                                         inNames >> firstCol >> secondCol; gobble(inNames);
 266                                         nameMap[firstCol] = getNumNames(secondCol);  //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
 267                                 }
 268                                 inNames.close();
 269                         }
 270
 271                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 272
 273                         if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
 274                         string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
 275                         string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 276                         string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
 277
 278                         outputNames.push_back(newTaxonomyFile);
 279                         outputNames.push_back(taxSummary);
 280
 281                         int start = time(NULL);
 282                         int numFastaSeqs = 0;
 283                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 284
 285 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 286                         if(processors == 1){
 287                                 ifstream inFASTA;
 288                                 openInputFile(fastaFileNames[s], inFASTA);
 289                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 290                                 inFASTA.close();
 291
 292                                 lines.push_back(new linePair(0, numFastaSeqs));
 293
 294                                 driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 295                         }
 296                         else{
 297                                 vector<int> positions;
 298                                 processIDS.resize(0);
 299
 300                                 ifstream inFASTA;
 301                                 openInputFile(fastaFileNames[s], inFASTA);
 302
 303                                 string input;
 304                                 while(!inFASTA.eof()){
 305                                         input = getline(inFASTA);
 306                                         if (input.length() != 0) {
 307                                                 if(input[0] == '>'){    int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);       }
 308                                         }
 309                                 }
 310                                 inFASTA.close();
 311
 312                                 numFastaSeqs = positions.size();
 313
 314                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 315
 316                                 for (int i = 0; i < processors; i++) {
 317                                         int startPos = positions[ i * numSeqsPerProcessor ];
 318                                         if(i == processors - 1){
 319                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 320                                         }
 321                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 322                                 }
 323                                 createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 324
 325                                 rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
 326                                 rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
 327
 328                                 for(int i=1;i<processors;i++){
 329                                         appendTaxFiles((newTaxonomyFile + toString(processIDS[i]) + ".temp"), newTaxonomyFile);
 330                                         appendTaxFiles((tempTaxonomyFile + toString(processIDS[i]) + ".temp"), tempTaxonomyFile);
 331                                         remove((newTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
 332                                         remove((tempTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
 333                                 }
 334
 335                         }
 336 #else
 337                         ifstream inFASTA;
 338                         openInputFile(fastaFileNames[s], inFASTA);
 339                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 340                         inFASTA.close();
 341
 342                         lines.push_back(new linePair(0, numFastaSeqs));
 343
 344                         driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 345 #endif
 346                         //make taxonomy tree from new taxonomy file
 347                         PhyloTree taxaBrowser;
 348
 349                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete classify; return 0; }
 350
 351                         ifstream in;
 352                         openInputFile(tempTaxonomyFile, in);
 353
 354                         //read in users taxonomy file and add sequences to tree
 355                         string name, taxon;
 356                         while(!in.eof()){
 357                                 in >> name >> taxon; gobble(in);
 358
 359                                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } remove(tempTaxonomyFile.c_str()); delete classify; return 0; }
 360
 361                                 if (namefile != "") {
 362                                         itNames = nameMap.find(name);
 363
 364                                         if (itNames == nameMap.end()) {
 365                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 366                                         }else{
 367                                                 for (int i = 0; i < itNames->second; i++) {
 368                                                         taxaBrowser.addSeqToTree(name+toString(i), taxon);  //add it as many times as there are identical seqs
 369                                                 }
 370                                         }
 371                                 }else {  taxaBrowser.addSeqToTree(name, taxon);  } //add it once
 372                         }
 373                         in.close();
 374
 375                         taxaBrowser.assignHeirarchyIDs(0);
 376
 377                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } remove(tempTaxonomyFile.c_str()); delete classify; return 0; }
 378
 379                         taxaBrowser.binUnclassified();
 380
 381                         remove(tempTaxonomyFile.c_str());
 382
 383                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete classify; return 0; }
 384
 385
 386                         //print summary file
 387                         ofstream outTaxTree;
 388                         openOutputFile(taxSummary, outTaxTree);
 389                         taxaBrowser.print(outTaxTree);
 390                         outTaxTree.close();
 391
 392                         //output taxonomy with the unclassified bins added
 393                         ifstream inTax;
 394                         openInputFile(newTaxonomyFile, inTax);
 395
 396                         ofstream outTax;
 397                         string unclass = newTaxonomyFile + ".unclass.temp";
 398                         openOutputFile(unclass, outTax);
 399
 400                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 401                         int maxLevel = taxaBrowser.getMaxLevel();
 402
 403                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 404                         while (!inTax.eof()) {
 405                                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
 406
 407                                 inTax >> name >> taxon; gobble(inTax);
 408
 409                                 string newTax = addUnclassifieds(taxon, maxLevel);
 410
 411                                 outTax << name << '\t' << newTax << endl;
 412                         }
 413                         inTax.close();
 414                         outTax.close();
 415
 416                         remove(newTaxonomyFile.c_str());
 417                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 418
 419                         m->mothurOutEndLine();
 420                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 421                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 422                         m->mothurOutEndLine();
 423
 424
 425                         m->mothurOutEndLine();
 426                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 427                 }
 428
 429                 delete classify;
 430                 return 0;
 431         }
 432         catch(exception& e) {
 433                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 434                 exit(1);
 435         }
 436 }
 437
 438 /**************************************************************************************************/
 439 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 440         try{
 441                 string newTax, taxon;
 442                 int level = 0;
 443
 444                 //keep what you have counting the levels
 445                 while (tax.find_first_of(';') != -1) {
 446                         //get taxon
 447                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 448                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 449                         newTax += taxon;
 450                         level++;
 451                 }
 452
 453                 //add "unclassified" until you reach maxLevel
 454                 while (level < maxlevel) {
 455                         newTax += "unclassified;";
 456                         level++;
 457                 }
 458
 459                 return newTax;
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 463                 exit(1);
 464         }
 465 }
 466
 467 /**************************************************************************************************/
 468
 469 void ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
 470         try {
 471 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 472                 int process = 0;
 473                 //              processIDS.resize(0);
 474
 475                 //loop through and create all the processes you want
 476                 while (process != processors) {
 477                         int pid = fork();
 478
 479                         if (pid > 0) {
 480                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 481                                 process++;
 482                         }else if (pid == 0){
 483                                 driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
 484                                 exit(0);
 485                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 486                 }
 487
 488                 //force parent to wait until all the processes are done
 489                 for (int i=0;i<processors;i++) {
 490                         int temp = processIDS[i];
 491                         wait(&temp);
 492                 }
 493 #endif
 494         }
 495         catch(exception& e) {
 496                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 497                 exit(1);
 498         }
 499 }
 500 /**************************************************************************************************/
 501
 502 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
 503         try{
 504
 505                 ofstream output;
 506                 ifstream input;
 507                 openOutputFileAppend(filename, output);
 508                 openInputFile(temp, input);
 509
 510                 while(char c = input.get()){
 511                         if(input.eof())         {       break;                  }
 512                         else                            {       output << c;    }
 513                 }
 514
 515                 input.close();
 516                 output.close();
 517         }
 518         catch(exception& e) {
 519                 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
 520                 exit(1);
 521         }
 522 }
 523
 524 //**********************************************************************************************************************
 525
 526 int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName, string filename){
 527         try {
 528                 ofstream outTax;
 529                 openOutputFile(taxFName, outTax);
 530
 531                 ofstream outTaxSimple;
 532                 openOutputFile(tempTFName, outTaxSimple);
 533
 534                 ifstream inFASTA;
 535                 openInputFile(filename, inFASTA);
 536
 537                 inFASTA.seekg(line->start);
 538
 539                 string taxonomy;
 540
 541                 for(int i=0;i<line->numSeqs;i++){
 542                         if (m->control_pressed) { return 0; }
 543
 544                         Sequence* candidateSeq = new Sequence(inFASTA);
 545
 546                         if (candidateSeq->getName() != "") {
 547                                 taxonomy = classify->getTaxonomy(candidateSeq);
 548
 549                                 if (m->control_pressed) { delete candidateSeq; return 0; }
 550
 551                                 if (taxonomy != "bad seq") {
 552                                         //output confidence scores or not
 553                                         if (probs) {
 554                                                 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
 555                                         }else{
 556                                                 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 557                                         }
 558
 559                                         outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 560                                 }
 561                         }
 562                         delete candidateSeq;
 563
 564                         if((i+1) % 100 == 0){
 565                                 m->mothurOut("Classifying sequence " + toString(i+1)); m->mothurOutEndLine();
 566                         }
 567                 }
 568
 569                 inFASTA.close();
 570                 outTax.close();
 571                 outTaxSimple.close();
 572
 573                 return 1;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "ClassifySeqsCommand", "driver");
 577                 exit(1);
 578         }
 579 }
 580
 581 /**************************************************************************************************/