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         //simplfy labels
 238         set<string> newLabels;
 239         for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {  newLabels.insert(m->getSimpleLabel(*it)); }
 240         labels = newLabels;
 241
 242         if (m->debug) { m->mothurOut("[DEBUG]: numlabels = " + toString(labels.size()) + "\n"); }
 243
 244                 if (m->control_pressed) { return 0; }
 245
 246                 //read through the correct file and output lines you want to keep
 247                 if (constaxonomyfile != "")     {               readClassifyOtu();      }
 248                 if (corraxesfile != "")         {               readCorrAxes();         }
 249                 if (otucorrfile != "")          {               readOtuAssociation();   }
 250         if (listfile != "")         {           readList();             }
 251         if (sharedfile != "")           {               readShared();           }
 252
 253         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 254
 255         //output files created by command
 256                 m->mothurOutEndLine();
 257                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 258                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 259                 m->mothurOutEndLine();
 260
 261         string current = "";
 262         itTypes = outputTypes.find("list");
 263         if (itTypes != outputTypes.end()) {
 264             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 265         }
 266
 267         itTypes = outputTypes.find("shared");
 268         if (itTypes != outputTypes.end()) {
 269             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 270         }
 271
 272         return 0;
 273     }
 274         catch(exception& e) {
 275                 m->errorOut(e, "GetOtuLabelsCommand", "execute");
 276                 exit(1);
 277         }
 278 }
 279 //**********************************************************************************************************************
 280 int RemoveOtuLabelsCommand::readClassifyOtu(){
 281         try {
 282                 string thisOutputDir = outputDir;
 283                 if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
 284                 map<string, string> variables;
 285         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
 286         variables["[extension]"] = m->getExtension(constaxonomyfile);
 287                 string outputFileName = getOutputFileName("constaxonomy", variables);
 288                 ofstream out;
 289                 m->openOutputFile(outputFileName, out);
 290
 291                 ifstream in;
 292                 m->openInputFile(constaxonomyfile, in);
 293
 294                 bool wroteSomething = false;
 295                 int removedCount = 0;
 296
 297         //read headers
 298         string headers = m->getline(in); m->gobble(in);
 299         out << headers << endl;
 300
 301         while (!in.eof()) {
 302
 303             if (m->control_pressed) { break; }
 304
 305             string otu = ""; string tax = "unknown";
 306             int size = 0;
 307
 308             in >> otu >> size >> tax; m->gobble(in);
 309
 310             if (m->debug) { m->mothurOut("[DEBUG]: " + otu + toString(size) + tax + "\n"); }
 311
 312             if (labels.count(m->getSimpleLabel(otu)) == 0) {
 313                                 wroteSomething = true;
 314                 out << otu << '\t' << size << '\t' << tax << endl;
 315             }else {  removedCount++;  }
 316         }
 317         in.close();
 318         out.close();
 319
 320                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 321                 outputNames.push_back(outputFileName);  outputTypes["constaxonomy"].push_back(outputFileName);
 322
 323                 m->mothurOut("Removed " + toString(removedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
 324
 325                 return 0;
 326
 327         }
 328         catch(exception& e) {
 329                 m->errorOut(e, "RemoveOtuLabelsCommand", "readClassifyOtu");
 330                 exit(1);
 331         }
 332 }
 333 //**********************************************************************************************************************
 334 int RemoveOtuLabelsCommand::readOtuAssociation(){
 335         try {
 336                 string thisOutputDir = outputDir;
 337                 if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
 338         map<string, string> variables;
 339         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
 340         variables["[extension]"] = m->getExtension(otucorrfile);
 341                 string outputFileName = getOutputFileName("otucorr", variables);
 342                 ofstream out;
 343                 m->openOutputFile(outputFileName, out);
 344
 345                 ifstream in;
 346                 m->openInputFile(otucorrfile, in);
 347
 348                 bool wroteSomething = false;
 349                 int removedCount = 0;
 350
 351         //read headers
 352         string headers = m->getline(in); m->gobble(in);
 353         out << headers << endl;
 354
 355         while (!in.eof()) {
 356
 357             if (m->control_pressed) { break; }
 358
 359             string otu1 = "";
 360             string otu2 = "";
 361             in >> otu1 >> otu2;
 362             string line = m->getline(in); m->gobble(in);
 363
 364             if ((labels.count(m->getSimpleLabel(otu1)) == 0) && (labels.count(m->getSimpleLabel(otu2)) == 0)){
 365                                 wroteSomething = true;
 366
 367                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
 368             }else { removedCount++; }
 369         }
 370         in.close();
 371         out.close();
 372
 373                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 374                 outputNames.push_back(outputFileName);  outputTypes["otucorr"].push_back(outputFileName);
 375
 376                 m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
 377
 378                 return 0;
 379
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "RemoveOtuLabelsCommand", "readOtuAssociation");
 383                 exit(1);
 384         }
 385 }
 386 //**********************************************************************************************************************
 387 int RemoveOtuLabelsCommand::readCorrAxes(){
 388         try {
 389                 string thisOutputDir = outputDir;
 390                 if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
 391         map<string, string> variables;
 392         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
 393         variables["[extension]"] = m->getExtension(corraxesfile);
 394                 string outputFileName = getOutputFileName("corraxes", variables);
 395                 ofstream out;
 396                 m->openOutputFile(outputFileName, out);
 397
 398
 399                 ifstream in;
 400                 m->openInputFile(corraxesfile, in);
 401
 402                 bool wroteSomething = false;
 403                 int removedCount = 0;
 404
 405         //read headers
 406         string headers = m->getline(in); m->gobble(in);
 407         out << headers << endl;
 408
 409         while (!in.eof()) {
 410
 411             if (m->control_pressed) { break; }
 412
 413             string otu = "";
 414             in >> otu;
 415             string line = m->getline(in); m->gobble(in);
 416
 417             if (labels.count(m->getSimpleLabel(otu)) == 0) {
 418                                 wroteSomething = true;
 419
 420                 out << otu << '\t' << line << endl;
 421             }else { removedCount++; }
 422         }
 423         in.close();
 424         out.close();
 425
 426                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 427                 outputNames.push_back(outputFileName);  outputTypes["corraxes"].push_back(outputFileName);
 428
 429                 m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
 430
 431                 return 0;
 432
 433         }
 434         catch(exception& e) {
 435                 m->errorOut(e, "RemoveOtuLabelsCommand", "readCorrAxes");
 436                 exit(1);
 437         }
 438 }
 439 //**********************************************************************************************************************
 440 int RemoveOtuLabelsCommand::readShared(){
 441         try {
 442
 443         getShared();
 444
 445         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 446
 447         vector<string> newLabels;
 448
 449         //create new "filtered" lookup
 450         vector<SharedRAbundVector*> newLookup;
 451         for (int i = 0; i < lookup.size(); i++) {
 452             SharedRAbundVector* temp = new SharedRAbundVector();
 453                         temp->setLabel(lookup[i]->getLabel());
 454                         temp->setGroup(lookup[i]->getGroup());
 455                         newLookup.push_back(temp);
 456         }
 457
 458         bool wroteSomething = false;
 459         int numRemoved = 0;
 460         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 461
 462             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; }
 463
 464             //is this otu on the list
 465             if (labels.count(m->getSimpleLabel(m->currentSharedBinLabels[i])) == 0) {
 466                 wroteSomething = true;
 467                 newLabels.push_back(m->currentSharedBinLabels[i]);
 468                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
 469                     newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
 470                 }
 471             }else { numRemoved++; }
 472         }
 473
 474         string thisOutputDir = outputDir;
 475                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 476         map<string, string> variables;
 477                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 478         variables["[extension]"] = m->getExtension(sharedfile);
 479         variables["[distance]"] = lookup[0]->getLabel();
 480                 string outputFileName = getOutputFileName("shared", variables);
 481         ofstream out;
 482                 m->openOutputFile(outputFileName, out);
 483                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 484
 485                 for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
 486
 487         m->currentSharedBinLabels = newLabels;
 488
 489                 newLookup[0]->printHeaders(out);
 490
 491                 for (int i = 0; i < newLookup.size(); i++) {
 492                         out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
 493                         newLookup[i]->print(out);
 494                 }
 495                 out.close();
 496
 497         for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
 498
 499         if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine();  }
 500
 501                 m->mothurOut("Removed " + toString(numRemoved) + " OTUs from your shared file."); m->mothurOutEndLine();
 502
 503         return 0;
 504     }
 505         catch(exception& e) {
 506                 m->errorOut(e, "RemoveOtuLabelsCommand", "readShared");
 507                 exit(1);
 508         }
 509 }
 510 //**********************************************************************************************************************
 511 int RemoveOtuLabelsCommand::readList(){
 512         try {
 513         getListVector();
 514
 515         if (m->control_pressed) { delete list; return 0;}
 516
 517         ListVector newList;
 518         newList.setLabel(list->getLabel());
 519         int removedCount = 0;
 520         bool wroteSomething = false;
 521
 522         vector<string> binLabels = list->getLabels();
 523         vector<string> newLabels;
 524         for (int i = 0; i < list->getNumBins(); i++) {
 525
 526             if (m->control_pressed) { delete list; return 0;}
 527
 528             if (labels.count(m->getSimpleLabel(binLabels[i])) == 0) {
 529                 newList.push_back(list->get(i));
 530                 newLabels.push_back(binLabels[i]);
 531             }else { removedCount++; }
 532         }
 533
 534         string thisOutputDir = outputDir;
 535                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 536         map<string, string> variables;
 537                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 538         variables["[extension]"] = m->getExtension(listfile);
 539         variables["[distance]"] = list->getLabel();
 540                 string outputFileName = getOutputFileName("list", variables);
 541                 ofstream out;
 542                 m->openOutputFile(outputFileName, out);
 543
 544                 delete list;
 545         //print new listvector
 546         if (newList.getNumBins() != 0) {
 547             wroteSomething = true;
 548             newList.setLabels(newLabels);
 549             newList.printHeaders(out);
 550             newList.print(out);
 551         }
 552                 out.close();
 553
 554                 if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine();  }
 555                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 556
 557                 m->mothurOut("Removed " + toString(removedCount) + " OTUs from your list file."); m->mothurOutEndLine();
 558
 559         return 0;
 560     }
 561     catch(exception& e) {
 562         m->errorOut(e, "RemoveOtuLabelsCommand", "readList");
 563         exit(1);
 564     }
 565 }
 566 //**********************************************************************************************************************
 567 int RemoveOtuLabelsCommand::getListVector(){
 568         try {
 569                 InputData input(listfile, "list");
 570                 list = input.getListVector();
 571                 string lastLabel = list->getLabel();
 572
 573                 if (label == "") { label = lastLabel;  return 0; }
 574
 575                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 576                 set<string> labels; labels.insert(label);
 577                 set<string> processedLabels;
 578                 set<string> userLabels = labels;
 579
 580                 //as long as you are not at the end of the file or done wih the lines you want
 581                 while((list != NULL) && (userLabels.size() != 0)) {
 582                         if (m->control_pressed) {  return 0;  }
 583
 584                         if(labels.count(list->getLabel()) == 1){
 585                                 processedLabels.insert(list->getLabel());
 586                                 userLabels.erase(list->getLabel());
 587                                 break;
 588                         }
 589
 590                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 591                                 string saveLabel = list->getLabel();
 592
 593                                 delete list;
 594                                 list = input.getListVector(lastLabel);
 595
 596                                 processedLabels.insert(list->getLabel());
 597                                 userLabels.erase(list->getLabel());
 598
 599                                 //restore real lastlabel to save below
 600                                 list->setLabel(saveLabel);
 601                                 break;
 602                         }
 603
 604                         lastLabel = list->getLabel();
 605
 606                         //get next line to process
 607                         //prevent memory leak
 608                         delete list;
 609                         list = input.getListVector();
 610                 }
 611
 612
 613                 if (m->control_pressed) {  return 0;  }
 614
 615                 //output error messages about any remaining user labels
 616                 set<string>::iterator it;
 617                 bool needToRun = false;
 618                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 619                         m->mothurOut("Your file does not include the label " + *it);
 620                         if (processedLabels.count(lastLabel) != 1) {
 621                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 622                                 needToRun = true;
 623                         }else {
 624                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 625                         }
 626                 }
 627
 628                 //run last label if you need to
 629                 if (needToRun == true)  {
 630                         delete list;
 631                         list = input.getListVector(lastLabel);
 632                 }
 633
 634                 return 0;
 635         }
 636         catch(exception& e) {
 637                 m->errorOut(e, "RemoveOtuLabelsCommand", "getListVector");
 638                 exit(1);
 639         }
 640 }
 641 //**********************************************************************************************************************
 642 int RemoveOtuLabelsCommand::getShared(){
 643         try {
 644                 InputData input(sharedfile, "sharedfile");
 645                 lookup = input.getSharedRAbundVectors();
 646                 string lastLabel = lookup[0]->getLabel();
 647
 648                 if (label == "") { label = lastLabel;  return 0; }
 649
 650                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 651                 set<string> labels; labels.insert(label);
 652                 set<string> processedLabels;
 653                 set<string> userLabels = labels;
 654
 655                 //as long as you are not at the end of the file or done wih the lines you want
 656                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 657                         if (m->control_pressed) {   return 0;  }
 658
 659                         if(labels.count(lookup[0]->getLabel()) == 1){
 660                                 processedLabels.insert(lookup[0]->getLabel());
 661                                 userLabels.erase(lookup[0]->getLabel());
 662                                 break;
 663                         }
 664
 665                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 666                                 string saveLabel = lookup[0]->getLabel();
 667
 668                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 669                                 lookup = input.getSharedRAbundVectors(lastLabel);
 670
 671                                 processedLabels.insert(lookup[0]->getLabel());
 672                                 userLabels.erase(lookup[0]->getLabel());
 673
 674                                 //restore real lastlabel to save below
 675                                 lookup[0]->setLabel(saveLabel);
 676                                 break;
 677                         }
 678
 679                         lastLabel = lookup[0]->getLabel();
 680
 681                         //get next line to process
 682                         //prevent memory leak
 683                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 684                         lookup = input.getSharedRAbundVectors();
 685                 }
 686
 687
 688                 if (m->control_pressed) {  return 0;  }
 689
 690                 //output error messages about any remaining user labels
 691                 set<string>::iterator it;
 692                 bool needToRun = false;
 693                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 694                         m->mothurOut("Your file does not include the label " + *it);
 695                         if (processedLabels.count(lastLabel) != 1) {
 696                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 697                                 needToRun = true;
 698                         }else {
 699                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 700                         }
 701                 }
 702
 703                 //run last label if you need to
 704                 if (needToRun == true)  {
 705                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 706                         lookup = input.getSharedRAbundVectors(lastLabel);
 707                 }
 708
 709                 return 0;
 710         }
 711         catch(exception& e) {
 712                 m->errorOut(e, "RemoveOtuLabelsCommand", "getShared");
 713                 exit(1);
 714         }
 715 }
 716 //**********************************************************************************************************************
 717
 718
 719