removeotulabelscommand.cpp

   1 //
   2 //  removeotulabels.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 5/21/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "removeotulabelscommand.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> RemoveOtuLabelsCommand::setParameters(){
  13         try {
  14         CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
  15         CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false); parameters.push_back(pconstaxonomy);
  16                 CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
  17         CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
  18         CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false, true); parameters.push_back(plist);
  19         CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared);
  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, "RemoveOtuLabelsCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string RemoveOtuLabelsCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The remove.otulabels command can be used to remove specific otus with the output from classify.otu, otu.association, or corr.axes. It can also be used to select a set of otus from a shared or list file.\n";
  38                 helpString += "The remove.otulabels parameters are: constaxonomy, otucorr, corraxes, shared, list, label and accnos.\n";
  39                 helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n";
  40         helpString += "The otucorr parameter is input the results of the otu.association command.\n";
  41         helpString += "The corraxes parameter is input the results of the corr.axes command.\n";
  42         helpString += "The label parameter is used to analyze specific labels in your input. \n";
  43                 helpString += "The remove.otulabels commmand should be in the following format: \n";
  44                 helpString += "remove.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "RemoveOtuLabelsCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string RemoveOtuLabelsCommand::getOutputPattern(string type) {
  54     try {
  55         string pattern = "";
  56
  57         if (type == "constaxonomy")         {   pattern = "[filename],pick,[extension]";                }
  58         else if (type == "otucorr")         {   pattern = "[filename],pick,[extension]";                }
  59         else if (type == "corraxes")        {   pattern = "[filename],pick,[extension]";                }
  60         else if (type == "list")            {   pattern = "[filename],[distance],pick,[extension]";     }
  61         else if (type == "shared")          {   pattern = "[filename],[distance],pick,[extension]";     }
  62         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  63
  64         return pattern;
  65     }
  66     catch(exception& e) {
  67         m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputPattern");
  68         exit(1);
  69     }
  70 }
  71 //**********************************************************************************************************************
  72 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76         vector<string> tempOutNames;
  77                 outputTypes["constaxonomy"] = tempOutNames;
  78         outputTypes["otucorr"] = tempOutNames;
  79         outputTypes["corraxes"] = tempOutNames;
  80         outputTypes["shared"] = tempOutNames;
  81         outputTypes["list"] = tempOutNames;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(string option)  {
  90         try {
  91                 abort = false; calledHelp = false;
  92
  93                 //allow user to run help
  94                 if(option == "help") { help(); abort = true; calledHelp = true; }
  95                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  96
  97                 else {
  98                         //valid paramters for this command
  99                         vector<string> myArray = setParameters();
 100
 101                         OptionParser parser(option);
 102                         map<string,string> parameters = parser.getParameters();
 103
 104                         ValidParameters validParameter;
 105                         map<string,string>::iterator it;
 106                         //check to make sure all parameters are valid for command
 107                         for (it = parameters.begin(); it != parameters.end(); it++) {
 108                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 109                         }
 110
 111
 112                         //if the user changes the input directory command factory will send this info to us in the output parameter
 113                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 114                         if (inputDir == "not found"){   inputDir = "";          }
 115                         else {
 116
 117                 //edit file types below to include only the types you added as parameters
 118
 119                                 string path;
 120                 it = parameters.find("constaxonomy");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["constaxonomy"] = inputDir + it->second;             }
 126                                 }
 127
 128                 it = parameters.find("accnos");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 134                                 }
 135
 136                 it = parameters.find("corraxes");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["corraxes"] = inputDir + it->second;         }
 142                                 }
 143
 144                 it = parameters.find("otucorr");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["otucorr"] = inputDir + it->second;          }
 150                                 }
 151
 152                 it = parameters.find("list");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 158                                 }
 159
 160                 it = parameters.find("shared");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 166                                 }
 167             }
 168
 169             vector<string> tempOutNames;
 170             outputTypes["constaxonomy"] = tempOutNames;
 171             outputTypes["otucorr"] = tempOutNames;
 172             outputTypes["corraxes"] = tempOutNames;
 173             outputTypes["shared"] = tempOutNames;
 174             outputTypes["list"] = tempOutNames;
 175
 176
 177                         //check for parameters
 178             accnosfile = validParameter.validFile(parameters, "accnos", true);
 179                         if (accnosfile == "not open") { abort = true; }
 180                         else if (accnosfile == "not found") {
 181                                 accnosfile = m->getAccnosFile();
 182                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 183                                 else {
 184                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 185                                         abort = true;
 186                                 }
 187                         }else { m->setAccnosFile(accnosfile); }
 188
 189                         constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
 190                         if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; }
 191                         else if (constaxonomyfile == "not found") {  constaxonomyfile = "";  }
 192
 193             corraxesfile = validParameter.validFile(parameters, "corraxes", true);
 194                         if (corraxesfile == "not open") { corraxesfile = ""; abort = true; }
 195                         else if (corraxesfile == "not found") {  corraxesfile = "";  }
 196
 197             otucorrfile = validParameter.validFile(parameters, "otucorr", true);
 198                         if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
 199                         else if (otucorrfile == "not found") {  otucorrfile = "";  }
 200
 201             listfile = validParameter.validFile(parameters, "list", true);
 202                         if (listfile == "not open") { listfile = ""; abort = true; }
 203                         else if (listfile == "not found") {  listfile = "";  }
 204             else { m->setListFile(listfile); }
 205
 206             sharedfile = validParameter.validFile(parameters, "shared", true);
 207                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 208                         else if (sharedfile == "not found") {  sharedfile = "";  }
 209             else { m->setSharedFile(sharedfile); }
 210
 211             //if the user changes the output directory command factory will send this info to us in the output parameter
 212                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){   outputDir = "";        }
 213
 214             if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "") && (sharedfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: constaxonomy, corraxes, otucorr, shared or list."); m->mothurOutEndLine(); abort = true; }
 215
 216             if ((sharedfile != "") || (listfile != "")) {
 217                 label = validParameter.validFile(parameters, "label", false);
 218                 if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
 219             }
 220                 }
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
 225                 exit(1);
 226         }
 227 }
 228 //**********************************************************************************************************************
 229
 230 int RemoveOtuLabelsCommand::execute(){
 231         try {
 232
 233                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 234
 235         //get labels you want to keep
 236                 labels = m->readAccnos(accnosfile);
 237
 238         if (m->debug) { m->mothurOut("[DEBUG]: numlabels = " + toString(labels.size()) + "\n"); }
 239
 240                 if (m->control_pressed) { return 0; }
 241
 242                 //read through the correct file and output lines you want to keep
 243                 if (constaxonomyfile != "")     {               readClassifyOtu();      }
 244                 if (corraxesfile != "")         {               readCorrAxes();         }
 245                 if (otucorrfile != "")          {               readOtuAssociation();   }
 246         if (listfile != "")         {           readList();             }
 247         if (sharedfile != "")           {               readShared();           }
 248
 249         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 250
 251         //output files created by command
 252                 m->mothurOutEndLine();
 253                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 254                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 255                 m->mothurOutEndLine();
 256
 257         string current = "";
 258         itTypes = outputTypes.find("list");
 259         if (itTypes != outputTypes.end()) {
 260             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 261         }
 262
 263         itTypes = outputTypes.find("shared");
 264         if (itTypes != outputTypes.end()) {
 265             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 266         }
 267
 268         return 0;
 269     }
 270         catch(exception& e) {
 271                 m->errorOut(e, "GetOtuLabelsCommand", "execute");
 272                 exit(1);
 273         }
 274 }
 275 //**********************************************************************************************************************
 276 int RemoveOtuLabelsCommand::readClassifyOtu(){
 277         try {
 278                 string thisOutputDir = outputDir;
 279                 if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
 280                 map<string, string> variables;
 281         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
 282         variables["[extension]"] = m->getExtension(constaxonomyfile);
 283                 string outputFileName = getOutputFileName("constaxonomy", variables);
 284                 ofstream out;
 285                 m->openOutputFile(outputFileName, out);
 286
 287                 ifstream in;
 288                 m->openInputFile(constaxonomyfile, in);
 289
 290                 bool wroteSomething = false;
 291                 int removedCount = 0;
 292
 293         //read headers
 294         string headers = m->getline(in); m->gobble(in);
 295         out << headers << endl;
 296
 297         while (!in.eof()) {
 298
 299             if (m->control_pressed) { break; }
 300
 301             string otu = ""; string tax = "unknown";
 302             int size = 0;
 303
 304             in >> otu >> size >> tax; m->gobble(in);
 305
 306             if (m->debug) { m->mothurOut("[DEBUG]: " + otu + toString(size) + tax + "\n"); }
 307
 308             if (labels.count(otu) == 0) {
 309                                 wroteSomething = true;
 310                 out << otu << '\t' << size << '\t' << tax << endl;
 311             }else {  removedCount++;  }
 312         }
 313         in.close();
 314         out.close();
 315
 316                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 317                 outputNames.push_back(outputFileName);  outputTypes["constaxonomy"].push_back(outputFileName);
 318
 319                 m->mothurOut("Removed " + toString(removedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
 320
 321                 return 0;
 322
 323         }
 324         catch(exception& e) {
 325                 m->errorOut(e, "RemoveOtuLabelsCommand", "readClassifyOtu");
 326                 exit(1);
 327         }
 328 }
 329 //**********************************************************************************************************************
 330 int RemoveOtuLabelsCommand::readOtuAssociation(){
 331         try {
 332                 string thisOutputDir = outputDir;
 333                 if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
 334         map<string, string> variables;
 335         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
 336         variables["[extension]"] = m->getExtension(otucorrfile);
 337                 string outputFileName = getOutputFileName("otucorr", variables);
 338                 ofstream out;
 339                 m->openOutputFile(outputFileName, out);
 340
 341                 ifstream in;
 342                 m->openInputFile(otucorrfile, in);
 343
 344                 bool wroteSomething = false;
 345                 int removedCount = 0;
 346
 347         //read headers
 348         string headers = m->getline(in); m->gobble(in);
 349         out << headers << endl;
 350
 351         while (!in.eof()) {
 352
 353             if (m->control_pressed) { break; }
 354
 355             string otu1 = "";
 356             string otu2 = "";
 357             in >> otu1 >> otu2;
 358             string line = m->getline(in); m->gobble(in);
 359
 360             if ((labels.count(otu1) == 0) && (labels.count(otu2) == 0)){
 361                                 wroteSomething = true;
 362
 363                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
 364             }else { removedCount++; }
 365         }
 366         in.close();
 367         out.close();
 368
 369                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 370                 outputNames.push_back(outputFileName);  outputTypes["otucorr"].push_back(outputFileName);
 371
 372                 m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
 373
 374                 return 0;
 375
 376         }
 377         catch(exception& e) {
 378                 m->errorOut(e, "RemoveOtuLabelsCommand", "readOtuAssociation");
 379                 exit(1);
 380         }
 381 }
 382 //**********************************************************************************************************************
 383 int RemoveOtuLabelsCommand::readCorrAxes(){
 384         try {
 385                 string thisOutputDir = outputDir;
 386                 if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
 387         map<string, string> variables;
 388         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
 389         variables["[extension]"] = m->getExtension(corraxesfile);
 390                 string outputFileName = getOutputFileName("corraxes", variables);
 391                 ofstream out;
 392                 m->openOutputFile(outputFileName, out);
 393
 394
 395                 ifstream in;
 396                 m->openInputFile(corraxesfile, in);
 397
 398                 bool wroteSomething = false;
 399                 int removedCount = 0;
 400
 401         //read headers
 402         string headers = m->getline(in); m->gobble(in);
 403         out << headers << endl;
 404
 405         while (!in.eof()) {
 406
 407             if (m->control_pressed) { break; }
 408
 409             string otu = "";
 410             in >> otu;
 411             string line = m->getline(in); m->gobble(in);
 412
 413             if (labels.count(otu) == 0) {
 414                                 wroteSomething = true;
 415
 416                 out << otu << '\t' << line << endl;
 417             }else { removedCount++; }
 418         }
 419         in.close();
 420         out.close();
 421
 422                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 423                 outputNames.push_back(outputFileName);  outputTypes["corraxes"].push_back(outputFileName);
 424
 425                 m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
 426
 427                 return 0;
 428
 429         }
 430         catch(exception& e) {
 431                 m->errorOut(e, "RemoveOtuLabelsCommand", "readCorrAxes");
 432                 exit(1);
 433         }
 434 }
 435 //**********************************************************************************************************************
 436 int RemoveOtuLabelsCommand::readShared(){
 437         try {
 438
 439         getShared();
 440
 441         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 442
 443         vector<string> newLabels;
 444
 445         //create new "filtered" lookup
 446         vector<SharedRAbundVector*> newLookup;
 447         for (int i = 0; i < lookup.size(); i++) {
 448             SharedRAbundVector* temp = new SharedRAbundVector();
 449                         temp->setLabel(lookup[i]->getLabel());
 450                         temp->setGroup(lookup[i]->getGroup());
 451                         newLookup.push_back(temp);
 452         }
 453
 454         bool wroteSomething = false;
 455         int numRemoved = 0;
 456         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 457
 458             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
 459
 460             //is this otu on the list
 461             if (labels.count(m->currentBinLabels[i]) == 0) {
 462                 wroteSomething = true;
 463                 newLabels.push_back(m->currentBinLabels[i]);
 464                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
 465                     newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
 466                 }
 467             }else { numRemoved++; }
 468         }
 469
 470         string thisOutputDir = outputDir;
 471                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 472         map<string, string> variables;
 473                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 474         variables["[extension]"] = m->getExtension(sharedfile);
 475         variables["[distance]"] = lookup[0]->getLabel();
 476                 string outputFileName = getOutputFileName("shared", variables);
 477         ofstream out;
 478                 m->openOutputFile(outputFileName, out);
 479                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 480
 481                 for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
 482
 483         m->currentBinLabels = newLabels;
 484
 485                 newLookup[0]->printHeaders(out);
 486
 487                 for (int i = 0; i < newLookup.size(); i++) {
 488                         out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
 489                         newLookup[i]->print(out);
 490                 }
 491                 out.close();
 492
 493         for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
 494
 495         if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine();  }
 496
 497                 m->mothurOut("Removed " + toString(numRemoved) + " OTUs from your shared file."); m->mothurOutEndLine();
 498
 499         return 0;
 500     }
 501         catch(exception& e) {
 502                 m->errorOut(e, "RemoveOtuLabelsCommand", "readShared");
 503                 exit(1);
 504         }
 505 }
 506 //**********************************************************************************************************************
 507 int RemoveOtuLabelsCommand::readList(){
 508         try {
 509         getListVector();
 510
 511         if (m->control_pressed) { delete list; return 0;}
 512
 513         ListVector newList;
 514         newList.setLabel(list->getLabel());
 515         int removedCount = 0;
 516         bool wroteSomething = false;
 517         string snumBins = toString(list->getNumBins());
 518
 519         for (int i = 0; i < list->getNumBins(); i++) {
 520
 521             if (m->control_pressed) { delete list; return 0;}
 522
 523             //create a label for this otu
 524             string otuLabel = "Otu";
 525             string sbinNumber = toString(i+1);
 526             if (sbinNumber.length() < snumBins.length()) {
 527                 int diff = snumBins.length() - sbinNumber.length();
 528                 for (int h = 0; h < diff; h++) { otuLabel += "0"; }
 529             }
 530             otuLabel += sbinNumber;
 531
 532             if (labels.count(otuLabel) == 0) {
 533                 newList.push_back(list->get(i));
 534             }else { removedCount++; }
 535         }
 536
 537         string thisOutputDir = outputDir;
 538                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 539         map<string, string> variables;
 540                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 541         variables["[extension]"] = m->getExtension(listfile);
 542         variables["[distance]"] = list->getLabel();
 543                 string outputFileName = getOutputFileName("list", variables);
 544                 ofstream out;
 545                 m->openOutputFile(outputFileName, out);
 546
 547                 delete list;
 548         //print new listvector
 549         if (newList.getNumBins() != 0) {
 550             wroteSomething = true;
 551             newList.print(out);
 552         }
 553                 out.close();
 554
 555                 if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine();  }
 556                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 557
 558                 m->mothurOut("Removed " + toString(removedCount) + " OTUs from your list file."); m->mothurOutEndLine();
 559
 560         return 0;
 561     }
 562     catch(exception& e) {
 563         m->errorOut(e, "RemoveOtuLabelsCommand", "readList");
 564         exit(1);
 565     }
 566 }
 567 //**********************************************************************************************************************
 568 int RemoveOtuLabelsCommand::getListVector(){
 569         try {
 570                 InputData input(listfile, "list");
 571                 list = input.getListVector();
 572                 string lastLabel = list->getLabel();
 573
 574                 if (label == "") { label = lastLabel;  return 0; }
 575
 576                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 577                 set<string> labels; labels.insert(label);
 578                 set<string> processedLabels;
 579                 set<string> userLabels = labels;
 580
 581                 //as long as you are not at the end of the file or done wih the lines you want
 582                 while((list != NULL) && (userLabels.size() != 0)) {
 583                         if (m->control_pressed) {  return 0;  }
 584
 585                         if(labels.count(list->getLabel()) == 1){
 586                                 processedLabels.insert(list->getLabel());
 587                                 userLabels.erase(list->getLabel());
 588                                 break;
 589                         }
 590
 591                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 592                                 string saveLabel = list->getLabel();
 593
 594                                 delete list;
 595                                 list = input.getListVector(lastLabel);
 596
 597                                 processedLabels.insert(list->getLabel());
 598                                 userLabels.erase(list->getLabel());
 599
 600                                 //restore real lastlabel to save below
 601                                 list->setLabel(saveLabel);
 602                                 break;
 603                         }
 604
 605                         lastLabel = list->getLabel();
 606
 607                         //get next line to process
 608                         //prevent memory leak
 609                         delete list;
 610                         list = input.getListVector();
 611                 }
 612
 613
 614                 if (m->control_pressed) {  return 0;  }
 615
 616                 //output error messages about any remaining user labels
 617                 set<string>::iterator it;
 618                 bool needToRun = false;
 619                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 620                         m->mothurOut("Your file does not include the label " + *it);
 621                         if (processedLabels.count(lastLabel) != 1) {
 622                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 623                                 needToRun = true;
 624                         }else {
 625                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 626                         }
 627                 }
 628
 629                 //run last label if you need to
 630                 if (needToRun == true)  {
 631                         delete list;
 632                         list = input.getListVector(lastLabel);
 633                 }
 634
 635                 return 0;
 636         }
 637         catch(exception& e) {
 638                 m->errorOut(e, "RemoveOtuLabelsCommand", "getListVector");
 639                 exit(1);
 640         }
 641 }
 642 //**********************************************************************************************************************
 643 int RemoveOtuLabelsCommand::getShared(){
 644         try {
 645                 InputData input(sharedfile, "sharedfile");
 646                 lookup = input.getSharedRAbundVectors();
 647                 string lastLabel = lookup[0]->getLabel();
 648
 649                 if (label == "") { label = lastLabel;  return 0; }
 650
 651                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 652                 set<string> labels; labels.insert(label);
 653                 set<string> processedLabels;
 654                 set<string> userLabels = labels;
 655
 656                 //as long as you are not at the end of the file or done wih the lines you want
 657                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 658                         if (m->control_pressed) {   return 0;  }
 659
 660                         if(labels.count(lookup[0]->getLabel()) == 1){
 661                                 processedLabels.insert(lookup[0]->getLabel());
 662                                 userLabels.erase(lookup[0]->getLabel());
 663                                 break;
 664                         }
 665
 666                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 667                                 string saveLabel = lookup[0]->getLabel();
 668
 669                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 670                                 lookup = input.getSharedRAbundVectors(lastLabel);
 671
 672                                 processedLabels.insert(lookup[0]->getLabel());
 673                                 userLabels.erase(lookup[0]->getLabel());
 674
 675                                 //restore real lastlabel to save below
 676                                 lookup[0]->setLabel(saveLabel);
 677                                 break;
 678                         }
 679
 680                         lastLabel = lookup[0]->getLabel();
 681
 682                         //get next line to process
 683                         //prevent memory leak
 684                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 685                         lookup = input.getSharedRAbundVectors();
 686                 }
 687
 688
 689                 if (m->control_pressed) {  return 0;  }
 690
 691                 //output error messages about any remaining user labels
 692                 set<string>::iterator it;
 693                 bool needToRun = false;
 694                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 695                         m->mothurOut("Your file does not include the label " + *it);
 696                         if (processedLabels.count(lastLabel) != 1) {
 697                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 698                                 needToRun = true;
 699                         }else {
 700                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 701                         }
 702                 }
 703
 704                 //run last label if you need to
 705                 if (needToRun == true)  {
 706                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 707                         lookup = input.getSharedRAbundVectors(lastLabel);
 708                 }
 709
 710                 return 0;
 711         }
 712         catch(exception& e) {
 713                 m->errorOut(e, "RemoveOtuLabelsCommand", "getShared");
 714                 exit(1);
 715         }
 716 }
 717 //**********************************************************************************************************************
 718
 719
 720