createdatabasecommand.cpp

   1 //
   2 //  createdatabasecommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 3/28/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "createdatabasecommand.h"
  10 #include "inputdata.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> CreateDatabaseCommand::setParameters(){
  14         try {
  15                 CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,true,true); parameters.push_back(pfasta);
  16                 CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
  17                 CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pcontaxonomy);
  18                 CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(plist);
  19         CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(pshared);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
  21                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "CreateDatabaseCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string CreateDatabaseCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The create.database command reads a list file or a shared file, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
  39                 helpString += "The create.database command parameters are repfasta, list, shared, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required.\n";
  40         helpString += "The repfasta file is fasta file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
  41         helpString += "The repname file is the name file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
  42         helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile).\n";
  43         helpString += "The group file is optional and will just give you the abundance breakdown by group.\n";
  44         helpString += "The label parameter allows you to specify a label to be used from your listfile.\n";
  45         helpString += "NOTE: Make SURE the repfasta, repnames and contaxonomy are for the same label as the listfile.\n";
  46         helpString += "The create.database command should be in the following format: \n";
  47                 helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
  48                 helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, name=final.an.0.03.rep.names, list=fina.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 string CreateDatabaseCommand::getOutputPattern(string type) {
  59     try {
  60         string pattern = "";
  61
  62         if (type == "database") {  pattern = "[filename],database"; }
  63         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  64
  65         return pattern;
  66     }
  67     catch(exception& e) {
  68         m->errorOut(e, "CreateDatabaseCommand", "getOutputPattern");
  69         exit(1);
  70     }
  71 }
  72 //**********************************************************************************************************************
  73 CreateDatabaseCommand::CreateDatabaseCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 vector<string> tempOutNames;
  78                 outputTypes["database"] = tempOutNames;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
  82                 exit(1);
  83         }
  84 }
  85
  86 //**********************************************************************************************************************
  87 CreateDatabaseCommand::CreateDatabaseCommand(string option)  {
  88         try{
  89                 abort = false; calledHelp = false;
  90
  91                 //allow user to run help
  92                 if (option == "help") {
  93                         help(); abort = true; calledHelp = true;
  94                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  95                 else {
  96                         vector<string> myArray = setParameters();
  97
  98                         OptionParser parser(option);
  99                         map<string, string> parameters = parser.getParameters();
 100
 101                         ValidParameters validParameter;
 102                         map<string, string>::iterator it;
 103
 104                         //check to make sure all parameters are valid for command
 105                         for (it = parameters.begin(); it != parameters.end(); it++) {
 106                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 107                         }
 108
 109                         //initialize outputTypes
 110                         vector<string> tempOutNames;
 111                         outputTypes["database"] = tempOutNames;
 112
 113                         //if the user changes the input directory command factory will send this info to us in the output parameter
 114                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 115                         if (inputDir == "not found"){   inputDir = "";          }
 116                         else {
 117                                 string path;
 118                                 it = parameters.find("list");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 124                                 }
 125
 126                                 it = parameters.find("repname");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["repname"] = inputDir + it->second;          }
 132                                 }
 133
 134                                 it = parameters.find("contaxonomy");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 140                                 }
 141
 142                                 it = parameters.find("repfasta");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["repfasta"] = inputDir + it->second;         }
 148                                 }
 149
 150                                 it = parameters.find("group");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 156                                 }
 157
 158                 it = parameters.find("shared");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 164                                 }
 165                         }
 166
 167
 168                         //if the user changes the output directory command factory will send this info to us in the output parameter
 169                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 170
 171                         //check for required parameters
 172                         listfile = validParameter.validFile(parameters, "list", true);
 173                         if (listfile == "not found") {  listfile = "";                  }
 174                         else if (listfile == "not open") { listfile = ""; abort = true; }
 175                         else { m->setListFile(listfile); }
 176
 177             sharedfile = validParameter.validFile(parameters, "shared", true);
 178                         if (sharedfile == "not found") {        sharedfile = "";                        }
 179                         else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 180                         else { m->setSharedFile(sharedfile); }
 181
 182             if ((sharedfile == "") && (listfile == "")) {
 183                                 //is there are current file available for either of these?
 184                                 //give priority to list, then shared
 185                                 listfile = m->getListFile();
 186                                 if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 187                                 else {
 188                                         sharedfile = m->getSharedFile();
 189                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 190                                         else {
 191                                                 m->mothurOut("No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
 192                                                 abort = true;
 193                                         }
 194                                 }
 195                         }
 196                         else if ((sharedfile != "") && (listfile != "")) { m->mothurOut("When executing a create.database command you must enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true; }
 197
 198             if (sharedfile != "") { if (outputDir == "") { outputDir = m->hasPath(sharedfile); } }
 199             else { if (outputDir == "") { outputDir = m->hasPath(listfile); } }
 200
 201                         contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 202                         if (contaxonomyfile == "not found") {  //if there is a current list file, use it
 203                contaxonomyfile = "";  m->mothurOut("The contaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 204                         }
 205                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 206
 207             repfastafile = validParameter.validFile(parameters, "repfasta", true);
 208                         if (repfastafile == "not found") {  //if there is a current list file, use it
 209                 repfastafile = "";  m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 210                         }
 211                         else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
 212
 213             repnamesfile = validParameter.validFile(parameters, "repname", true);
 214                         if (repnamesfile == "not found") {  //if there is a current list file, use it
 215                 repnamesfile = "";  m->mothurOut("The repnames parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 216                         }
 217                         else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
 218
 219                         groupfile = validParameter.validFile(parameters, "group", true);
 220                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 221                         else if (groupfile == "not found") { groupfile = ""; }
 222                         else { m->setGroupFile(groupfile); }
 223
 224                         //check for optional parameter and set defaults
 225                         // ...at some point should added some additional type checking...
 226             label = validParameter.validFile(parameters, "label", false);
 227                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
 228         }
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
 232                 exit(1);
 233         }
 234 }
 235 //**********************************************************************************************************************
 236 int CreateDatabaseCommand::execute(){
 237         try {
 238
 239                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 240
 241         //taxonomies holds the taxonomy info for each Otu
 242         //classifyOtuSizes holds the size info of each Otu to help with error checking
 243         vector<string> taxonomies;
 244         vector<string> otuLabels;
 245         vector<int> classifyOtuSizes = readTax(taxonomies, otuLabels);
 246
 247         if (m->control_pressed) { return 0; }
 248
 249         vector<Sequence> seqs;
 250         vector<int> repOtusSizes = readFasta(seqs);
 251
 252         if (m->control_pressed) { return 0; }
 253
 254         //names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
 255         map<string, string> repNames;
 256         int numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
 257
 258         //are there the same number of otus in the fasta and name files
 259         if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file.  These should match.\n"); m->control_pressed = true; }
 260
 261         if (m->control_pressed) { return 0; }
 262
 263         //are there the same number of OTUs in the tax and fasta file
 264         if (classifyOtuSizes.size() != repOtusSizes.size()) { m->mothurOut("[ERROR]: you have " + toString(classifyOtuSizes.size()) + " taxonomies in your contaxonomy file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file.  These should match.\n"); m->control_pressed = true; }
 265
 266         if (m->control_pressed) { return 0; }
 267
 268         //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
 269         for (int i = 0; i < classifyOtuSizes.size(); i++) {
 270             if (classifyOtuSizes[i] != repOtusSizes[i]) {
 271                m->mothurOut("[ERROR]: OTU size info does not match for bin " + toString(i+1) + ". The contaxonomy file indicated the OTU represented " + toString(classifyOtuSizes[i]) + " sequences, but the repfasta file had " + toString(repOtusSizes[i]) + ".  These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true;
 272             }
 273         }
 274
 275         if (m->control_pressed) { return 0; }
 276
 277
 278         map<string, string> variables;
 279         if (listfile != "") {  variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); }
 280         else { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); }
 281         string outputFileName = getOutputFileName("database", variables);
 282         outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
 283
 284         ofstream out;
 285         m->openOutputFile(outputFileName, out);
 286
 287         string header = "OTUNumber\tAbundance\t";
 288
 289
 290         if (listfile != "") {
 291             //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
 292             ListVector* list = getList();
 293
 294             if (otuLabels.size() != list->getNumBins()) {
 295                 m->mothurOut("[ERROR]: you have " + toString(otuLabels.size()) + " otus in your contaxonomy file, but your list file has " + toString(list->getNumBins()) + " otus. These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true;  }
 296
 297             if (m->control_pressed) { delete list; return 0; }
 298
 299             GroupMap* groupmap = NULL;
 300             if (groupfile != "") {
 301                 groupmap = new GroupMap(groupfile);
 302                 groupmap->readMap();
 303             }
 304
 305             if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
 306
 307             if (groupfile != "") {
 308                 header = "OTUNumber\t";
 309                 for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
 310             }
 311             header += "repSeqName\trepSeq\tOTUConTaxonomy";
 312             out << header << endl;
 313
 314             for (int i = 0; i < list->getNumBins(); i++) {
 315
 316                 if (m->control_pressed) { break; }
 317
 318                 out << otuLabels[i] << '\t';
 319
 320                 vector<string> binNames;
 321                 string bin = list->get(i);
 322
 323                 map<string, string>::iterator it = repNames.find(bin);
 324                 if (it == repNames.end()) {
 325                     m->mothurOut("[ERROR: OTU " + otuLabels[i] + " is not in the repnames file. Make sure you are using files for the same distance.\n"); m->control_pressed = true;   break;
 326                 }
 327
 328                 m->splitAtComma(bin, binNames);
 329
 330                 //sanity check
 331                 if (binNames.size() != classifyOtuSizes[i]) {
 332                     m->mothurOut("[ERROR: OTU " + otuLabels[i] + " contains " + toString(binNames.size()) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[i]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true;   break;
 333                 }
 334
 335                 //output abundances
 336                 if (groupfile != "") {
 337                     string groupAbunds = "";
 338                     map<string, int> counts;
 339                     //initialize counts to 0
 340                     for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
 341
 342                     //find abundances by group
 343                     bool error = false;
 344                     for (int j = 0; j < binNames.size(); j++) {
 345                         string group = groupmap->getGroup(binNames[j]);
 346                         if (group == "not found") {
 347                             m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
 348                             error = true;
 349                         }else { counts[group]++; }
 350                     }
 351
 352                     //output counts
 353                     for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t';  }
 354
 355                     if (error) { m->control_pressed = true; }
 356                 }else { out << binNames.size() << '\t'; }
 357
 358                 //output repSeq
 359                 out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
 360             }
 361
 362
 363             delete list;
 364             if (groupfile != "") { delete groupmap; }
 365
 366         }else {
 367             vector<SharedRAbundVector*> lookup = getShared();
 368
 369             header = "OTUNumber\t";
 370             for (int i = 0; i < lookup.size(); i++) { header += lookup[i]->getGroup() + '\t'; }
 371             header += "repSeqName\trepSeq\tOTUConTaxonomy";
 372             out << header << endl;
 373
 374             for (int h = 0; h < lookup[0]->getNumBins(); h++) {
 375
 376                 if (m->control_pressed) { break; }
 377
 378                 int index = findIndex(otuLabels, m->currentBinLabels[h]);
 379                 if (index == -1) {  m->mothurOut("[ERROR]: " + m->currentBinLabels[h] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
 380
 381                 if (m->control_pressed) { break; }
 382
 383                 out << otuLabels[index] << '\t';
 384
 385                 int totalAbund = 0;
 386                 for (int i = 0; i < lookup.size(); i++) {
 387                     int abund = lookup[i]->getAbundance(h);
 388                     totalAbund += abund;
 389                     out << abund << '\t';
 390                 }
 391
 392                 //sanity check
 393                 if (totalAbund != classifyOtuSizes[index]) {
 394                     m->mothurOut("[WARNING]: OTU " + m->currentBinLabels[h] + " contains " + toString(totalAbund) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); //m->control_pressed = true;   break;
 395                 }
 396
 397                 //output repSeq
 398                 out << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
 399             }
 400         }
 401         out.close();
 402         if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 403
 404         m->mothurOutEndLine();
 405                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 406                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 407                 m->mothurOutEndLine();
 408
 409         return 0;
 410
 411     }
 412         catch(exception& e) {
 413                 m->errorOut(e, "CreateDatabaseCommand", "execute");
 414                 exit(1);
 415         }
 416 }
 417 //**********************************************************************************************************************
 418 int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
 419         try {
 420         int index = -1;
 421         for (int i = 0; i < otuLabels.size(); i++) {
 422             if (otuLabels[i] == label) { index = i; break; }
 423         }
 424                 return index;
 425     }
 426         catch(exception& e) {
 427                 m->errorOut(e, "CreateDatabaseCommand", "findIndex");
 428                 exit(1);
 429         }
 430 }
 431 //**********************************************************************************************************************
 432 vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<string>& otuLabels){
 433         try {
 434
 435         vector<int> sizes;
 436
 437         ifstream in;
 438         m->openInputFile(contaxonomyfile, in);
 439
 440         //read headers
 441         m->getline(in);
 442
 443         while (!in.eof()) {
 444
 445             if (m->control_pressed) { break; }
 446
 447             string otu = ""; string tax = "unknown";
 448             int size = 0;
 449
 450             in >> otu >> size >> tax; m->gobble(in);
 451
 452             sizes.push_back(size);
 453             taxonomies.push_back(tax);
 454             otuLabels.push_back(otu);
 455         }
 456         in.close();
 457
 458         return sizes;
 459     }
 460         catch(exception& e) {
 461                 m->errorOut(e, "CreateDatabaseCommand", "readTax");
 462                 exit(1);
 463         }
 464 }
 465 //**********************************************************************************************************************
 466 vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
 467         try {
 468
 469         vector<int> sizes;
 470
 471         ifstream in;
 472         m->openInputFile(repfastafile, in);
 473
 474         while (!in.eof()) {
 475
 476             if (m->control_pressed) { break; }
 477
 478             string binInfo;
 479             Sequence seq(in, binInfo, true);  m->gobble(in);
 480
 481             //the binInfo should look like - binNumber|size ie. 1|200 if it is binNumber|size|group then the user gave us the wrong repfasta file
 482             vector<string> info;
 483             m->splitAtChar(binInfo, info, '|');
 484             if (info.size() != 2) { m->mothurOut("[ERROR]: your repfasta file is not the right format.  The create database command is designed to be used with the output from get.oturep.  When running get.oturep you can not use a group file, because mothur is only expecting one representative sequence per OTU and when you use a group file with get.oturep a representative is found for each group.\n");  m->control_pressed = true; break;}
 485
 486             int size = 0;
 487             m->mothurConvert(info[1], size);
 488
 489             sizes.push_back(size);
 490             seqs.push_back(seq);
 491         }
 492         in.close();
 493
 494         return sizes;
 495     }
 496         catch(exception& e) {
 497                 m->errorOut(e, "CreateDatabaseCommand", "readFasta");
 498                 exit(1);
 499         }
 500 }
 501 //**********************************************************************************************************************
 502 ListVector* CreateDatabaseCommand::getList(){
 503         try {
 504                 InputData* input = new InputData(listfile, "list");
 505                 ListVector* list = input->getListVector();
 506                 string lastLabel = list->getLabel();
 507
 508                 if (label == "") { label = lastLabel; delete input; return list; }
 509
 510                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 511                 set<string> labels; labels.insert(label);
 512                 set<string> processedLabels;
 513                 set<string> userLabels = labels;
 514
 515                 //as long as you are not at the end of the file or done wih the lines you want
 516                 while((list != NULL) && (userLabels.size() != 0)) {
 517                         if (m->control_pressed) {  delete input; return list;  }
 518
 519                         if(labels.count(list->getLabel()) == 1){
 520                                 processedLabels.insert(list->getLabel());
 521                                 userLabels.erase(list->getLabel());
 522                                 break;
 523                         }
 524
 525                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 526                                 string saveLabel = list->getLabel();
 527
 528                                 delete list;
 529                                 list = input->getListVector(lastLabel);
 530
 531                                 processedLabels.insert(list->getLabel());
 532                                 userLabels.erase(list->getLabel());
 533
 534                                 //restore real lastlabel to save below
 535                                 list->setLabel(saveLabel);
 536                                 break;
 537                         }
 538
 539                         lastLabel = list->getLabel();
 540
 541                         //get next line to process
 542                         //prevent memory leak
 543                         delete list;
 544                         list = input->getListVector();
 545                 }
 546
 547
 548                 if (m->control_pressed) { delete input; return list;  }
 549
 550                 //output error messages about any remaining user labels
 551                 set<string>::iterator it;
 552                 bool needToRun = false;
 553                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 554                         m->mothurOut("Your file does not include the label " + *it);
 555                         if (processedLabels.count(lastLabel) != 1) {
 556                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 557                                 needToRun = true;
 558                         }else {
 559                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 560                         }
 561                 }
 562
 563                 //run last label if you need to
 564                 if (needToRun == true)  {
 565                         delete list;
 566                         list = input->getListVector(lastLabel);
 567                 }
 568
 569                 delete input;
 570
 571         return list;
 572     }
 573         catch(exception& e) {
 574                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 575                 exit(1);
 576         }
 577 }
 578 //**********************************************************************************************************************
 579 vector<SharedRAbundVector*> CreateDatabaseCommand::getShared(){
 580         try {
 581                 InputData input(sharedfile, "sharedfile");
 582                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 583                 string lastLabel = lookup[0]->getLabel();
 584
 585                 if (label == "") { label = lastLabel; return lookup; }
 586
 587                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 588                 set<string> labels; labels.insert(label);
 589                 set<string> processedLabels;
 590                 set<string> userLabels = labels;
 591
 592                 //as long as you are not at the end of the file or done wih the lines you want
 593                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 594                         if (m->control_pressed) {  return lookup;  }
 595
 596                         if(labels.count(lookup[0]->getLabel()) == 1){
 597                                 processedLabels.insert(lookup[0]->getLabel());
 598                                 userLabels.erase(lookup[0]->getLabel());
 599                                 break;
 600                         }
 601
 602                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 603                                 string saveLabel = lookup[0]->getLabel();
 604
 605                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 606                                 lookup = input.getSharedRAbundVectors(lastLabel);
 607
 608                                 processedLabels.insert(lookup[0]->getLabel());
 609                                 userLabels.erase(lookup[0]->getLabel());
 610
 611                                 //restore real lastlabel to save below
 612                                 lookup[0]->setLabel(saveLabel);
 613                                 break;
 614                         }
 615
 616                         lastLabel = lookup[0]->getLabel();
 617
 618                         //get next line to process
 619                         //prevent memory leak
 620                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 621                         lookup = input.getSharedRAbundVectors();
 622                 }
 623
 624
 625                 if (m->control_pressed) { return lookup;  }
 626
 627                 //output error messages about any remaining user labels
 628                 set<string>::iterator it;
 629                 bool needToRun = false;
 630                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 631                         m->mothurOut("Your file does not include the label " + *it);
 632                         if (processedLabels.count(lastLabel) != 1) {
 633                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 634                                 needToRun = true;
 635                         }else {
 636                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 637                         }
 638                 }
 639
 640                 //run last label if you need to
 641                 if (needToRun == true)  {
 642                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 643                         lookup = input.getSharedRAbundVectors(lastLabel);
 644                 }
 645
 646         return lookup;
 647     }
 648         catch(exception& e) {
 649                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 650                 exit(1);
 651         }
 652 }
 653
 654 //**********************************************************************************************************************
 655
 656