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