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",false,true); parameters.push_back(pfasta);
  16                 CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
  17                 CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
  18                 CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none",false,false); parameters.push_back(plist);
  19         CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none",false,false); 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::getOutputFileNameTag(string type, string inputName=""){
  59         try {
  60         string outputFileName = "";
  61                 map<string, vector<string> >::iterator it;
  62
  63         //is this a type this command creates
  64         it = outputTypes.find(type);
  65         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  66         else {
  67             if (type == "database") {  outputFileName =  "database"; }
  68             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  69         }
  70         return outputFileName;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "CreateDatabaseCommand", "getOutputFileNameTag");
  74                 exit(1);
  75         }
  76 }
  77
  78 //**********************************************************************************************************************
  79 CreateDatabaseCommand::CreateDatabaseCommand(){
  80         try {
  81                 abort = true; calledHelp = true;
  82                 setParameters();
  83                 vector<string> tempOutNames;
  84                 outputTypes["database"] = tempOutNames;
  85         }
  86         catch(exception& e) {
  87                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
  88                 exit(1);
  89         }
  90 }
  91
  92 //**********************************************************************************************************************
  93 CreateDatabaseCommand::CreateDatabaseCommand(string option)  {
  94         try{
  95                 abort = false; calledHelp = false;
  96
  97                 //allow user to run help
  98                 if (option == "help") {
  99                         help(); abort = true; calledHelp = true;
 100                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 101                 else {
 102                         vector<string> myArray = setParameters();
 103
 104                         OptionParser parser(option);
 105                         map<string, string> parameters = parser.getParameters();
 106
 107                         ValidParameters validParameter;
 108                         map<string, string>::iterator it;
 109
 110                         //check to make sure all parameters are valid for command
 111                         for (it = parameters.begin(); it != parameters.end(); it++) {
 112                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 113                         }
 114
 115                         //initialize outputTypes
 116                         vector<string> tempOutNames;
 117                         outputTypes["database"] = tempOutNames;
 118
 119                         //if the user changes the input directory command factory will send this info to us in the output parameter
 120                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 121                         if (inputDir == "not found"){   inputDir = "";          }
 122                         else {
 123                                 string path;
 124                                 it = parameters.find("list");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 130                                 }
 131
 132                                 it = parameters.find("repname");
 133                                 //user has given a template file
 134                                 if(it != parameters.end()){
 135                                         path = m->hasPath(it->second);
 136                                         //if the user has not given a path then, add inputdir. else leave path alone.
 137                                         if (path == "") {       parameters["repname"] = inputDir + it->second;          }
 138                                 }
 139
 140                                 it = parameters.find("contaxonomy");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 146                                 }
 147
 148                                 it = parameters.find("repfasta");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["repfasta"] = inputDir + it->second;         }
 154                                 }
 155
 156                                 it = parameters.find("group");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 162                                 }
 163
 164                 it = parameters.find("shared");
 165                                 //user has given a template file
 166                                 if(it != parameters.end()){
 167                                         path = m->hasPath(it->second);
 168                                         //if the user has not given a path then, add inputdir. else leave path alone.
 169                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 170                                 }
 171                         }
 172
 173
 174                         //if the user changes the output directory command factory will send this info to us in the output parameter
 175                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 176
 177                         //check for required parameters
 178                         listfile = validParameter.validFile(parameters, "list", true);
 179                         if (listfile == "not found") {  listfile = "";                  }
 180                         else if (listfile == "not open") { listfile = ""; abort = true; }
 181                         else { m->setListFile(listfile); }
 182
 183             sharedfile = validParameter.validFile(parameters, "shared", true);
 184                         if (sharedfile == "not found") {        sharedfile = "";                        }
 185                         else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 186                         else { m->setSharedFile(sharedfile); }
 187
 188             if ((sharedfile == "") && (listfile == "")) {
 189                                 //is there are current file available for either of these?
 190                                 //give priority to list, then shared
 191                                 listfile = m->getListFile();
 192                                 if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 193                                 else {
 194                                         sharedfile = m->getSharedFile();
 195                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 196                                         else {
 197                                                 m->mothurOut("No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
 198                                                 abort = true;
 199                                         }
 200                                 }
 201                         }
 202                         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; }
 203
 204             if (sharedfile != "") { if (outputDir == "") { outputDir = m->hasPath(sharedfile); } }
 205             else { if (outputDir == "") { outputDir = m->hasPath(listfile); } }
 206
 207                         contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 208                         if (contaxonomyfile == "not found") {  //if there is a current list file, use it
 209                contaxonomyfile = "";  m->mothurOut("The contaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 210                         }
 211                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 212
 213             repfastafile = validParameter.validFile(parameters, "repfasta", true);
 214                         if (repfastafile == "not found") {  //if there is a current list file, use it
 215                 repfastafile = "";  m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 216                         }
 217                         else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
 218
 219             repnamesfile = validParameter.validFile(parameters, "repname", true);
 220                         if (repnamesfile == "not found") {  //if there is a current list file, use it
 221                 repnamesfile = "";  m->mothurOut("The repnames parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 222                         }
 223                         else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
 224
 225                         groupfile = validParameter.validFile(parameters, "group", true);
 226                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 227                         else if (groupfile == "not found") { groupfile = ""; }
 228                         else { m->setGroupFile(groupfile); }
 229
 230                         //check for optional parameter and set defaults
 231                         // ...at some point should added some additional type checking...
 232             label = validParameter.validFile(parameters, "label", false);
 233                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
 234         }
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
 238                 exit(1);
 239         }
 240 }
 241 //**********************************************************************************************************************
 242 int CreateDatabaseCommand::execute(){
 243         try {
 244
 245                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 246
 247         //taxonomies holds the taxonomy info for each Otu
 248         //classifyOtuSizes holds the size info of each Otu to help with error checking
 249         vector<string> taxonomies;
 250         vector<string> otuLabels;
 251         vector<int> classifyOtuSizes = readTax(taxonomies, otuLabels);
 252
 253         if (m->control_pressed) { return 0; }
 254
 255         vector<Sequence> seqs;
 256         vector<int> repOtusSizes = readFasta(seqs);
 257
 258         if (m->control_pressed) { return 0; }
 259
 260         //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.
 261         map<string, string> repNames;
 262         int numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
 263
 264         //are there the same number of otus in the fasta and name files
 265         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; }
 266
 267         if (m->control_pressed) { return 0; }
 268
 269         //are there the same number of OTUs in the tax and fasta file
 270         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; }
 271
 272         if (m->control_pressed) { return 0; }
 273
 274         //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
 275         for (int i = 0; i < classifyOtuSizes.size(); i++) {
 276             if (classifyOtuSizes[i] != repOtusSizes[i]) {
 277                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;
 278             }
 279         }
 280
 281         if (m->control_pressed) { return 0; }
 282
 283
 284         string outputFileName = "";
 285         if (listfile != "") { outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database"); }
 286         else { outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("database"); }
 287         outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
 288
 289         ofstream out;
 290         m->openOutputFile(outputFileName, out);
 291
 292         string header = "OTUNumber\tAbundance\t";
 293
 294
 295         if (listfile != "") {
 296             //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
 297             ListVector* list = getList();
 298
 299             if (otuLabels.size() != list->getNumBins()) {
 300                 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;  }
 301
 302             if (m->control_pressed) { delete list; return 0; }
 303
 304             GroupMap* groupmap = NULL;
 305             if (groupfile != "") {
 306                 groupmap = new GroupMap(groupfile);
 307                 groupmap->readMap();
 308             }
 309
 310             if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
 311
 312             if (groupfile != "") {
 313                 header = "OTUNumber\t";
 314                 for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
 315             }
 316             header += "repSeqName\trepSeq\tOTUConTaxonomy";
 317             out << header << endl;
 318
 319             for (int i = 0; i < list->getNumBins(); i++) {
 320
 321                 if (m->control_pressed) { break; }
 322
 323                 out << otuLabels[i] << '\t';
 324
 325                 vector<string> binNames;
 326                 string bin = list->get(i);
 327
 328                 map<string, string>::iterator it = repNames.find(bin);
 329                 if (it == repNames.end()) {
 330                     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;
 331                 }
 332
 333                 m->splitAtComma(bin, binNames);
 334
 335                 //sanity check
 336                 if (binNames.size() != classifyOtuSizes[i]) {
 337                     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;
 338                 }
 339
 340                 //output abundances
 341                 if (groupfile != "") {
 342                     string groupAbunds = "";
 343                     map<string, int> counts;
 344                     //initialize counts to 0
 345                     for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
 346
 347                     //find abundances by group
 348                     bool error = false;
 349                     for (int j = 0; j < binNames.size(); j++) {
 350                         string group = groupmap->getGroup(binNames[j]);
 351                         if (group == "not found") {
 352                             m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
 353                             error = true;
 354                         }else { counts[group]++; }
 355                     }
 356
 357                     //output counts
 358                     for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t';  }
 359
 360                     if (error) { m->control_pressed = true; }
 361                 }else { out << binNames.size() << '\t'; }
 362
 363                 //output repSeq
 364                 out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
 365             }
 366
 367
 368             delete list;
 369             if (groupfile != "") { delete groupmap; }
 370
 371         }else {
 372             vector<SharedRAbundVector*> lookup = getShared();
 373
 374             header = "OTUNumber\t";
 375             for (int i = 0; i < lookup.size(); i++) { header += lookup[i]->getGroup() + '\t'; }
 376             header += "repSeqName\trepSeq\tOTUConTaxonomy";
 377             out << header << endl;
 378
 379             for (int h = 0; h < lookup[0]->getNumBins(); h++) {
 380
 381                 if (m->control_pressed) { break; }
 382
 383                 int index = findIndex(otuLabels, m->currentBinLabels[h]);
 384                 if (index == -1) {  m->mothurOut("[ERROR]: " + m->currentBinLabels[h] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
 385
 386                 if (m->control_pressed) { break; }
 387
 388                 out << otuLabels[index] << '\t';
 389
 390                 int totalAbund = 0;
 391                 for (int i = 0; i < lookup.size(); i++) {
 392                     int abund = lookup[i]->getAbundance(h);
 393                     totalAbund += abund;
 394                     out << abund << '\t';
 395                 }
 396
 397                 //sanity check
 398                 if (totalAbund != classifyOtuSizes[index]) {
 399                     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;
 400                 }
 401
 402                 //output repSeq
 403                 out << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
 404             }
 405         }
 406         out.close();
 407         if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 408
 409         m->mothurOutEndLine();
 410                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 411                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 412                 m->mothurOutEndLine();
 413
 414         return 0;
 415
 416     }
 417         catch(exception& e) {
 418                 m->errorOut(e, "CreateDatabaseCommand", "execute");
 419                 exit(1);
 420         }
 421 }
 422 //**********************************************************************************************************************
 423 int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
 424         try {
 425         int index = -1;
 426         for (int i = 0; i < otuLabels.size(); i++) {
 427             if (otuLabels[i] == label) { index = i; break; }
 428         }
 429                 return index;
 430     }
 431         catch(exception& e) {
 432                 m->errorOut(e, "CreateDatabaseCommand", "findIndex");
 433                 exit(1);
 434         }
 435 }
 436 //**********************************************************************************************************************
 437 vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<string>& otuLabels){
 438         try {
 439
 440         vector<int> sizes;
 441
 442         ifstream in;
 443         m->openInputFile(contaxonomyfile, in);
 444
 445         //read headers
 446         m->getline(in);
 447
 448         while (!in.eof()) {
 449
 450             if (m->control_pressed) { break; }
 451
 452             string otu = ""; string tax = "unknown";
 453             int size = 0;
 454
 455             in >> otu >> size >> tax; m->gobble(in);
 456
 457             sizes.push_back(size);
 458             taxonomies.push_back(tax);
 459             otuLabels.push_back(otu);
 460         }
 461         in.close();
 462
 463         return sizes;
 464     }
 465         catch(exception& e) {
 466                 m->errorOut(e, "CreateDatabaseCommand", "readTax");
 467                 exit(1);
 468         }
 469 }
 470 //**********************************************************************************************************************
 471 vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
 472         try {
 473
 474         vector<int> sizes;
 475
 476         ifstream in;
 477         m->openInputFile(repfastafile, in);
 478
 479         while (!in.eof()) {
 480
 481             if (m->control_pressed) { break; }
 482
 483             string binInfo;
 484             Sequence seq(in, binInfo, true);  m->gobble(in);
 485
 486             //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
 487             vector<string> info;
 488             m->splitAtChar(binInfo, info, '|');
 489             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;}
 490
 491             int size = 0;
 492             m->mothurConvert(info[1], size);
 493
 494             sizes.push_back(size);
 495             seqs.push_back(seq);
 496         }
 497         in.close();
 498
 499         return sizes;
 500     }
 501         catch(exception& e) {
 502                 m->errorOut(e, "CreateDatabaseCommand", "readFasta");
 503                 exit(1);
 504         }
 505 }
 506 //**********************************************************************************************************************
 507 ListVector* CreateDatabaseCommand::getList(){
 508         try {
 509                 InputData* input = new InputData(listfile, "list");
 510                 ListVector* list = input->getListVector();
 511                 string lastLabel = list->getLabel();
 512
 513                 if (label == "") { label = lastLabel; delete input; return list; }
 514
 515                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 516                 set<string> labels; labels.insert(label);
 517                 set<string> processedLabels;
 518                 set<string> userLabels = labels;
 519
 520                 //as long as you are not at the end of the file or done wih the lines you want
 521                 while((list != NULL) && (userLabels.size() != 0)) {
 522                         if (m->control_pressed) {  delete input; return list;  }
 523
 524                         if(labels.count(list->getLabel()) == 1){
 525                                 processedLabels.insert(list->getLabel());
 526                                 userLabels.erase(list->getLabel());
 527                                 break;
 528                         }
 529
 530                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 531                                 string saveLabel = list->getLabel();
 532
 533                                 delete list;
 534                                 list = input->getListVector(lastLabel);
 535
 536                                 processedLabels.insert(list->getLabel());
 537                                 userLabels.erase(list->getLabel());
 538
 539                                 //restore real lastlabel to save below
 540                                 list->setLabel(saveLabel);
 541                                 break;
 542                         }
 543
 544                         lastLabel = list->getLabel();
 545
 546                         //get next line to process
 547                         //prevent memory leak
 548                         delete list;
 549                         list = input->getListVector();
 550                 }
 551
 552
 553                 if (m->control_pressed) { delete input; return list;  }
 554
 555                 //output error messages about any remaining user labels
 556                 set<string>::iterator it;
 557                 bool needToRun = false;
 558                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 559                         m->mothurOut("Your file does not include the label " + *it);
 560                         if (processedLabels.count(lastLabel) != 1) {
 561                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 562                                 needToRun = true;
 563                         }else {
 564                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 565                         }
 566                 }
 567
 568                 //run last label if you need to
 569                 if (needToRun == true)  {
 570                         delete list;
 571                         list = input->getListVector(lastLabel);
 572                 }
 573
 574                 delete input;
 575
 576         return list;
 577     }
 578         catch(exception& e) {
 579                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 580                 exit(1);
 581         }
 582 }
 583 //**********************************************************************************************************************
 584 vector<SharedRAbundVector*> CreateDatabaseCommand::getShared(){
 585         try {
 586                 InputData input(sharedfile, "sharedfile");
 587                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 588                 string lastLabel = lookup[0]->getLabel();
 589
 590                 if (label == "") { label = lastLabel; return lookup; }
 591
 592                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 593                 set<string> labels; labels.insert(label);
 594                 set<string> processedLabels;
 595                 set<string> userLabels = labels;
 596
 597                 //as long as you are not at the end of the file or done wih the lines you want
 598                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 599                         if (m->control_pressed) {  return lookup;  }
 600
 601                         if(labels.count(lookup[0]->getLabel()) == 1){
 602                                 processedLabels.insert(lookup[0]->getLabel());
 603                                 userLabels.erase(lookup[0]->getLabel());
 604                                 break;
 605                         }
 606
 607                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 608                                 string saveLabel = lookup[0]->getLabel();
 609
 610                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 611                                 lookup = input.getSharedRAbundVectors(lastLabel);
 612
 613                                 processedLabels.insert(lookup[0]->getLabel());
 614                                 userLabels.erase(lookup[0]->getLabel());
 615
 616                                 //restore real lastlabel to save below
 617                                 lookup[0]->setLabel(saveLabel);
 618                                 break;
 619                         }
 620
 621                         lastLabel = lookup[0]->getLabel();
 622
 623                         //get next line to process
 624                         //prevent memory leak
 625                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 626                         lookup = input.getSharedRAbundVectors();
 627                 }
 628
 629
 630                 if (m->control_pressed) { return lookup;  }
 631
 632                 //output error messages about any remaining user labels
 633                 set<string>::iterator it;
 634                 bool needToRun = false;
 635                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 636                         m->mothurOut("Your file does not include the label " + *it);
 637                         if (processedLabels.count(lastLabel) != 1) {
 638                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 639                                 needToRun = true;
 640                         }else {
 641                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 642                         }
 643                 }
 644
 645                 //run last label if you need to
 646                 if (needToRun == true)  {
 647                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 648                         lookup = input.getSharedRAbundVectors(lastLabel);
 649                 }
 650
 651         return lookup;
 652     }
 653         catch(exception& e) {
 654                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 655                 exit(1);
 656         }
 657 }
 658
 659 //**********************************************************************************************************************
 660
 661