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