consensusseqscommand.cpp

   1 /*
   2  *  consensusseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/23/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "consensusseqscommand.h"
  11 #include "sequence.hpp"
  12 #include "inputdata.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> ConsensusSeqsCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta", "list", "name", "label","outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "ConsensusSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 ConsensusSeqsCommand::ConsensusSeqsCommand(){
  28         try {
  29                 abort = true;
  30                 //initialize outputTypes
  31                 vector<string> tempOutNames;
  32                 outputTypes["fasta"] = tempOutNames;
  33                 outputTypes["name"] = tempOutNames;
  34                 outputTypes["summary"] = tempOutNames;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 vector<string> ConsensusSeqsCommand::getRequiredParameters(){
  43         try {
  44                 string Array[] =  {"fasta", "list"};
  45                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "ConsensusSeqsCommand", "getRequiredParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 vector<string> ConsensusSeqsCommand::getRequiredFiles(){
  55         try {
  56                 vector<string> myArray;
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
  61                 exit(1);
  62         }
  63 }
  64 //***************************************************************************************************************
  65 ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
  66         try {
  67                 abort = false;
  68                 allLines = 1;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; }
  72
  73                 else {
  74                         //valid paramters for this command
  75                         string Array[] =  {"fasta","list","name","label", "outputdir","inputdir"};
  76                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  77
  78                         OptionParser parser(option);
  79                         map<string,string> parameters = parser.getParameters();
  80
  81                         ValidParameters validParameter;
  82                         map<string,string>::iterator it;
  83
  84                         //check to make sure all parameters are valid for command
  85                         for (it = parameters.begin(); it != parameters.end(); it++) {
  86                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  87                         }
  88
  89                         //initialize outputTypes
  90                         vector<string> tempOutNames;
  91                         outputTypes["fasta"] = tempOutNames;
  92                         outputTypes["name"] = tempOutNames;
  93                         outputTypes["summary"] = tempOutNames;
  94
  95
  96                         //if the user changes the input directory command factory will send this info to us in the output parameter
  97                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  98                         if (inputDir == "not found"){   inputDir = "";          }
  99                         else {
 100                                 string path;
 101                                 it = parameters.find("fasta");
 102                                 //user has given a template file
 103                                 if(it != parameters.end()){
 104                                         path = m->hasPath(it->second);
 105                                         //if the user has not given a path then, add inputdir. else leave path alone.
 106                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 107                                 }
 108
 109                                 it = parameters.find("name");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 115                                 }
 116
 117                                 it = parameters.find("list");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 123                                 }
 124                         }
 125
 126
 127                         //check for parameters
 128                         fastafile = validParameter.validFile(parameters, "fasta", true);
 129                         if (fastafile == "not open") { abort = true; }
 130                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true;  }
 131
 132                         namefile = validParameter.validFile(parameters, "name", true);
 133                         if (namefile == "not open") { abort = true; }
 134                         else if (namefile == "not found") { namefile = ""; }
 135
 136                         listfile = validParameter.validFile(parameters, "list", true);
 137                         if (listfile == "not open") { abort = true; }
 138                         else if (listfile == "not found") { listfile = "";  }
 139
 140                         label = validParameter.validFile(parameters, "label", false);
 141                         if (label == "not found") { label = ""; }
 142                         else {
 143                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 144                                 else { allLines = 1;  }
 145                         }
 146
 147                         //if the user changes the output directory command factory will send this info to us in the output parameter
 148                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
 149
 150                 }
 151         }
 152         catch(exception& e) {
 153                 m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
 154                 exit(1);
 155         }
 156 }
 157 //**********************************************************************************************************************
 158
 159 void ConsensusSeqsCommand::help(){
 160         try {
 161                 m->mothurOut("The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n");
 162                 m->mothurOut("The consensus.seqs command parameters are fasta, list, name and label.\n");
 163                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
 164                 m->mothurOut("The list parameter allows you to enter a your list file. \n");
 165                 m->mothurOut("The name parameter allows you to enter a names file associated with the fasta file. \n");
 166                 m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
 167                 m->mothurOut("The consensus.seqs command should be in the following format: \n");
 168                 m->mothurOut("consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n");
 169                 m->mothurOut("Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n");
 170                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 171         }
 172         catch(exception& e) {
 173                 m->errorOut(e, "ConsensusSeqsCommand", "help");
 174                 exit(1);
 175         }
 176 }
 177
 178 //***************************************************************************************************************
 179
 180 ConsensusSeqsCommand::~ConsensusSeqsCommand(){  /*      do nothing      */      }
 181
 182 //***************************************************************************************************************
 183
 184 int ConsensusSeqsCommand::execute(){
 185         try{
 186
 187                 if (abort == true) { return 0; }
 188
 189                 readFasta();
 190
 191                 if (m->control_pressed) { return 0; }
 192
 193                 if (namefile != "") { readNames(); }
 194
 195                 if (m->control_pressed) { return 0; }
 196
 197
 198                 if (listfile == "") {
 199
 200                         ofstream outSummary;
 201                         string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
 202                         m->openOutputFile(outputSummaryFile, outSummary);
 203                         outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
 204                         outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
 205
 206                         outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
 207
 208                         ofstream outFasta;
 209                         string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
 210                         m->openOutputFile(outputFastaFile, outFasta);
 211                         outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
 212
 213                         vector<string> seqs;
 214                         int seqLength = 0;
 215                         for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
 216
 217                                 if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
 218
 219                                 string seq = fastaMap[it->second];
 220                                 seqs.push_back(seq);
 221
 222                                 if (seqLength == 0) { seqLength = seq.length(); }
 223                                 else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 224
 225                         }
 226
 227                         vector< vector<float> > percentages; percentages.resize(5);
 228                         for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
 229
 230                         string consSeq = "";
 231                         //get counts
 232                         for (int j = 0; j < seqLength; j++) {
 233
 234                                 if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
 235
 236                                 vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
 237                                 int numDots = 0;
 238
 239                                 for (int i = 0; i < seqs.size(); i++) {
 240
 241                                         if (seqs[i][j] == '.') { numDots++; }
 242
 243                                         char base = toupper(seqs[i][j]);
 244                                         if (base == 'A') { counts[0]++; }
 245                                         else if (base == 'T') { counts[1]++; }
 246                                         else if (base == 'G') { counts[2]++; }
 247                                         else if (base == 'C') { counts[3]++; }
 248                                         else { counts[4]++; }
 249                                 }
 250
 251                                 char conBase = '.';
 252                                 if (numDots != seqs.size()) { conBase = getBase(counts); }
 253
 254                                 consSeq += conBase;
 255
 256                                 percentages[0][j] = counts[0] / (float) seqs.size();
 257                                 percentages[1][j] = counts[1] / (float) seqs.size();
 258                                 percentages[2][j] = counts[2] / (float) seqs.size();
 259                                 percentages[3][j] = counts[3] / (float) seqs.size();
 260                                 percentages[4][j] = counts[4] / (float) seqs.size();
 261
 262                         }
 263
 264                         for (int j = 0; j < seqLength; j++) {
 265                                 outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
 266                         }
 267
 268
 269                         outFasta << ">conseq" << endl << consSeq << endl;
 270
 271                         outSummary.close(); outFasta.close();
 272
 273
 274                 }else {
 275
 276
 277                         InputData* input = new InputData(listfile, "list");
 278                         ListVector* list = input->getListVector();
 279
 280                         string lastLabel = list->getLabel();
 281                         set<string> processedLabels;
 282                         set<string> userLabels = labels;
 283
 284                         //as long as you are not at the end of the file or done wih the lines you want
 285                         while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 286
 287                                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete list; delete input;  return 0;  }
 288
 289                                 if(allLines == 1 || labels.count(list->getLabel()) == 1){
 290
 291                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 292
 293                                         processList(list);
 294
 295                                         processedLabels.insert(list->getLabel());
 296                                         userLabels.erase(list->getLabel());
 297                                 }
 298
 299                                 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 300                                         string saveLabel = list->getLabel();
 301
 302                                         delete list;
 303
 304                                         list = input->getListVector(lastLabel);
 305                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 306
 307                                         processList(list);
 308
 309                                         processedLabels.insert(list->getLabel());
 310                                         userLabels.erase(list->getLabel());
 311
 312                                         //restore real lastlabel to save below
 313                                         list->setLabel(saveLabel);
 314                                 }
 315
 316                                 lastLabel = list->getLabel();
 317
 318                                 delete list; list = NULL;
 319
 320                                 //get next line to process
 321                                 list = input->getListVector();
 322                         }
 323
 324
 325                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0;  }
 326
 327                         //output error messages about any remaining user labels
 328                         set<string>::iterator it;
 329                         bool needToRun = false;
 330                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 331                                 m->mothurOut("Your file does not include the label " + *it);
 332                                 if (processedLabels.count(lastLabel) != 1) {
 333                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 334                                         needToRun = true;
 335                                 }else {
 336                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 337                                 }
 338                         }
 339
 340                         //run last label if you need to
 341                         if (needToRun == true)  {
 342                                 if (list != NULL) { delete list; }
 343
 344                                 list = input->getListVector(lastLabel);
 345
 346                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 347
 348                                 processList(list);
 349
 350                                 delete list; list = NULL;
 351                         }
 352
 353                         if (list != NULL) { delete list; }
 354                         delete input;
 355                 }
 356
 357                 m->mothurOutEndLine();
 358                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 359                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 360                 m->mothurOutEndLine();
 361
 362
 363                 return 0;
 364
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "ConsensusSeqsCommand", "execute");
 368                 exit(1);
 369         }
 370 }
 371 //***************************************************************************************************************
 372
 373 int ConsensusSeqsCommand::processList(ListVector*& list){
 374         try{
 375
 376                 ofstream outSummary;
 377                 string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary";
 378                 m->openOutputFile(outputSummaryFile, outSummary);
 379                 outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
 380                 outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
 381
 382                 ofstream outName;
 383                 string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.names";
 384                 m->openOutputFile(outputNameFile, outName);
 385                 outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
 386
 387                 ofstream outFasta;
 388                 string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.fasta";
 389                 m->openOutputFile(outputFastaFile, outFasta);
 390                 outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
 391
 392                 outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
 393
 394                 for (int i = 0; i < list->getNumBins(); i++) {
 395
 396                         if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
 397
 398                         string bin = list->get(i);
 399
 400                         string newName = "";
 401                         string consSeq = getConsSeq(bin, outSummary, newName, i);
 402
 403                         outFasta << ">seq" << (i+1) << endl << consSeq << endl;
 404                         outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << newName << endl;
 405                 }
 406
 407                 outSummary.close(); outName.close(); outFasta.close();
 408
 409                 return 0;
 410
 411         }
 412         catch(exception& e) {
 413                 m->errorOut(e, "ConsensusSeqsCommand", "processList");
 414                 exit(1);
 415         }
 416 }
 417
 418 //***************************************************************************************************************
 419 //made this smart enough to owrk with unique or non unique list file
 420 string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, string& name, int binNumber){
 421         try{
 422
 423                 string consSeq = "";
 424                 bool error = false;
 425
 426                 //the whole bin is the second column if no names file, otherwise build it
 427                 name = bin;
 428                 if (namefile != "") { name = ""; }
 429
 430                 vector<string> binNames;
 431                 m->splitAtComma(bin, binNames);
 432
 433                 //get sequence strings for each name in the bin
 434                 vector<string> seqs;
 435
 436                 set<string> addedAlready;
 437                 int seqLength = 0;
 438                 for (int i = 0; i < binNames.size(); i++) {
 439
 440                         map<string, string>::iterator it;
 441
 442                         it = nameMap.find(binNames[i]);
 443                         if (it == nameMap.end()) {
 444                                 if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
 445                                 else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
 446                                 break;
 447                         }else {
 448
 449                                 //add sequence string to seqs vector to process below
 450                                 string seq = fastaMap[it->second];
 451                                 seqs.push_back(seq);
 452
 453                                 if (seqLength == 0) { seqLength = seq.length(); }
 454                                 else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); error = true; break; }
 455
 456                                 if (namefile != "") {
 457                                         //did we add this line from name file already?
 458                                         if (addedAlready.count(it->second) == 0) {
 459                                                 name += "," + nameFileMap[it->second];
 460                                                 addedAlready.insert(it->second);
 461                                         }
 462                                 }
 463
 464                         }
 465                 }
 466
 467                 if (error) { m->control_pressed = true; return consSeq; }
 468
 469                 if (namefile != "") { name = name.substr(1); }
 470
 471                 vector< vector<float> > percentages; percentages.resize(5);
 472                 for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
 473
 474                 //get counts
 475                 for (int j = 0; j < seqLength; j++) {
 476
 477                         if (m->control_pressed) { return consSeq; }
 478
 479                         vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
 480                         int numDots = 0;
 481
 482                         for (int i = 0; i < seqs.size(); i++) {
 483
 484                                 if (seqs[i][j] == '.') { numDots++; }
 485
 486                                 char base = toupper(seqs[i][j]);
 487                                 if (base == 'A') { counts[0]++; }
 488                                 else if (base == 'T') { counts[1]++; }
 489                                 else if (base == 'G') { counts[2]++; }
 490                                 else if (base == 'C') { counts[3]++; }
 491                                 else { counts[4]++; }
 492                         }
 493
 494                         char conBase = '.';
 495                         if (numDots != seqs.size()) { conBase = getBase(counts); }
 496
 497                         consSeq += conBase;
 498
 499                         percentages[0][j] = counts[0] / (float) seqs.size();
 500                         percentages[1][j] = counts[1] / (float) seqs.size();
 501                         percentages[2][j] = counts[2] / (float) seqs.size();
 502                         percentages[3][j] = counts[3] / (float) seqs.size();
 503                         percentages[4][j] = counts[4] / (float) seqs.size();
 504
 505                 }
 506
 507                 for (int j = 0; j < seqLength; j++) {
 508                         outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
 509                 }
 510
 511                 return consSeq;
 512
 513         }
 514         catch(exception& e) {
 515                 m->errorOut(e, "ConsensusSeqsCommand", "getConsSeq");
 516                 exit(1);
 517         }
 518 }
 519 //***************************************************************************************************************
 520
 521 char ConsensusSeqsCommand::getBase(vector<int> counts){  //A,T,G,C,Gap
 522         try{
 523                 /* A = adenine
 524                 * C = cytosine
 525                 * G = guanine
 526                 * T = thymine
 527                 * R = G A (purine)
 528                 * Y = T C (pyrimidine)
 529                 * K = G T (keto)
 530                 * M = A C (amino)
 531                 * S = G C (strong bonds)
 532                 * W = A T (weak bonds)
 533                 * B = G T C (all but A)
 534                 * D = G A T (all but C)
 535                 * H = A C T (all but G)
 536                 * V = G C A (all but T)
 537                 * N = A G C T (any) */
 538
 539                 char conBase = 'N';
 540
 541                 //any
 542                 if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'n'; }
 543                 //any no gap
 544                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'N'; }
 545                 //all but T
 546                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'v'; }
 547                 //all but T no gap
 548                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'V'; }
 549                 //all but G
 550                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'h'; }
 551                 //all but G no gap
 552                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'H'; }
 553                 //all but C
 554                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 'd'; }
 555                 //all but C no gap
 556                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'D'; }
 557                 //all but A
 558                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'b'; }
 559                 //all but A no gap
 560                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'B'; }
 561                 //W = A T (weak bonds)
 562                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 'w'; }
 563                 //W = A T (weak bonds) no gap
 564                 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'W'; }
 565                 //S = G C (strong bonds)
 566                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 's'; }
 567                 //S = G C (strong bonds) no gap
 568                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'S'; }
 569                 //M = A C (amino)
 570                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'm'; }
 571                 //M = A C (amino) no gap
 572                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'M'; }
 573                 //K = G T (keto)
 574                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 'k'; }
 575                 //K = G T (keto) no gap
 576                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'K'; }
 577                 //Y = T C (pyrimidine)
 578                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'y'; }
 579                 //Y = T C (pyrimidine) no gap
 580                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'Y'; }
 581                 //R = G A (purine)
 582                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 'r'; }
 583                 //R = G A (purine) no gap
 584                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'R'; }
 585                 //only A
 586                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 'a'; }
 587                 //only A no gap
 588                 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'A'; }
 589                 //only T
 590                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 't'; }
 591                 //only T no gap
 592                 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'T'; }
 593                 //only G
 594                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = 'g'; }
 595                 //only G no gap
 596                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'G'; }
 597                 //only C
 598                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'c'; }
 599                 //only C no gap
 600                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) {  conBase = 'C'; }
 601                 //only gap
 602                 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = '-'; }
 603                 else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
 604
 605                 return conBase;
 606
 607         }
 608         catch(exception& e) {
 609                 m->errorOut(e, "ConsensusSeqsCommand", "getBase");
 610                 exit(1);
 611         }
 612 }
 613
 614 //***************************************************************************************************************
 615
 616 int ConsensusSeqsCommand::readFasta(){
 617         try{
 618
 619                 ifstream in;
 620                 m->openInputFile(fastafile, in);
 621
 622                 while (!in.eof()) {
 623
 624                         if (m->control_pressed) { break; }
 625
 626                         Sequence seq(in); m->gobble(in);
 627                         string name = seq.getName();
 628
 629                         if (name != "") {
 630                                 fastaMap[name] = seq.getAligned();
 631                                 nameMap[name] = name; //set nameMap incase no names file
 632                                 nameFileMap[name] = name;
 633                         }
 634                 }
 635
 636                 in.close();
 637
 638                 return 0;
 639
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "ConsensusSeqsCommand", "readFasta");
 643                 exit(1);
 644         }
 645 }
 646 //***************************************************************************************************************
 647
 648 int ConsensusSeqsCommand::readNames(){
 649          try{
 650
 651                  ifstream in;
 652                  m->openInputFile(namefile, in);
 653
 654                  string thisname, repnames;
 655                  map<string, string>::iterator it;
 656
 657                  bool error = false;
 658
 659                  while(!in.eof()){
 660
 661                          if (m->control_pressed) { break; }
 662
 663                          in >> thisname;                m->gobble(in);          //read from first column
 664                          in >> repnames;                        //read from second column
 665
 666                          it = nameMap.find(thisname);
 667                          if (it != nameMap.end()) { //then this sequence was in the fastafile
 668
 669                                  vector<string> splitRepNames;
 670                                  m->splitAtComma(repnames, splitRepNames);
 671
 672                                  nameFileMap[thisname] = repnames;      //for later when outputting the new namesFile if the list file is unique
 673                                  for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
 674
 675                          }else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
 676
 677                          m->gobble(in);
 678                  }
 679
 680                  in.close();
 681
 682                  if (error) { m->control_pressed = true; }
 683
 684                  return 0;
 685
 686         }
 687          catch(exception& e) {
 688                  m->errorOut(e, "ConsensusSeqsCommand", "readNames");
 689                  exit(1);
 690          }
 691  }
 692
 693 //***************************************************************************************************************
 694
 695