makebiomcommand.cpp

   1 //
   2 //  makebiomcommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 4/16/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "makebiomcommand.h"
  10 #include "sharedrabundvector.h"
  11 #include "inputdata.h"
  12
  13 //taken from http://biom-format.org/documentation/biom_format.html
  14 /* Minimal Sparse
  15  {
  16  "id":null,
  17  "format": "Biological Observation Matrix 0.9.1",
  18  "format_url": "http://biom-format.org",
  19  "type": "OTU table",
  20  "generated_by": "QIIME revision 1.4.0-dev",
  21  "date": "2011-12-19T19:00:00",
  22  "rows":[
  23  {"id":"GG_OTU_1", "metadata":null},
  24  {"id":"GG_OTU_2", "metadata":null},
  25  {"id":"GG_OTU_3", "metadata":null},
  26  {"id":"GG_OTU_4", "metadata":null},
  27  {"id":"GG_OTU_5", "metadata":null}
  28  ],
  29  "columns": [
  30  {"id":"Sample1", "metadata":null},
  31  {"id":"Sample2", "metadata":null},
  32  {"id":"Sample3", "metadata":null},
  33  {"id":"Sample4", "metadata":null},
  34  {"id":"Sample5", "metadata":null},
  35  {"id":"Sample6", "metadata":null}
  36  ],
  37  "matrix_type": "sparse",
  38  "matrix_element_type": "int",
  39  "shape": [5, 6],
  40  "data":[[0,2,1],
  41  [1,0,5],
  42  [1,1,1],
  43  [1,3,2],
  44  [1,4,3],
  45  [1,5,1],
  46  [2,2,1],
  47  [2,3,4],
  48  [2,4,2],
  49  [3,0,2],
  50  [3,1,1],
  51  [3,2,1],
  52  [3,5,1],
  53  [4,1,1],
  54  [4,2,1]
  55  ]
  56  }
  57  */
  58 /* Minimal dense
  59  {
  60  "id":null,
  61  "format": "Biological Observation Matrix 0.9.1",
  62  "format_url": "http://biom-format.org",
  63  "type": "OTU table",
  64  "generated_by": "QIIME revision 1.4.0-dev",
  65  "date": "2011-12-19T19:00:00",
  66  "rows":[
  67  {"id":"GG_OTU_1", "metadata":null},
  68  {"id":"GG_OTU_2", "metadata":null},
  69  {"id":"GG_OTU_3", "metadata":null},
  70  {"id":"GG_OTU_4", "metadata":null},
  71  {"id":"GG_OTU_5", "metadata":null}
  72  ],
  73  "columns": [
  74  {"id":"Sample1", "metadata":null},
  75  {"id":"Sample2", "metadata":null},
  76  {"id":"Sample3", "metadata":null},
  77  {"id":"Sample4", "metadata":null},
  78  {"id":"Sample5", "metadata":null},
  79  {"id":"Sample6", "metadata":null}
  80  ],
  81  "matrix_type": "dense",
  82  "matrix_element_type": "int",
  83  "shape": [5,6],
  84  "data":  [[0,0,1,0,0,0],
  85  [5,1,0,2,3,1],
  86  [0,0,1,4,2,0],
  87  [2,1,1,0,0,1],
  88  [0,1,1,0,0,0]]
  89  }
  90  */
  91 //**********************************************************************************************************************
  92 vector<string> MakeBiomCommand::setParameters(){
  93         try {
  94                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
  95         CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcontaxonomy);
  96                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  97                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  98                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  99                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 100         CommandParameter pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "",false,false); parameters.push_back(pmatrixtype);
 101
 102                 vector<string> myArray;
 103                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
 104                 return myArray;
 105         }
 106         catch(exception& e) {
 107                 m->errorOut(e, "MakeBiomCommand", "setParameters");
 108                 exit(1);
 109         }
 110 }
 111 //**********************************************************************************************************************
 112 string MakeBiomCommand::getHelpString(){
 113         try {
 114                 string helpString = "";
 115                 helpString += "The make.biom command parameters are shared, groups, matrixtype and label.  shared is required, unless you have a valid current file.\n";
 116                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
 117                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
 118                 helpString += "The matrixtype parameter allows you to select what type you would like to make. Choices are sparse and dense, default is sparse.\n";
 119                 helpString += "The make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\n";
 120         helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance.  ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled after the classify.otu command was run on the list and taxonomy file.\n";
 121                 helpString += "Example make.biom(shared=abrecovery.an.shared, groups=A-B-C).\n";
 122                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
 123                 helpString += "The make.biom command outputs a .biom file.\n";
 124                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
 125                 return helpString;
 126         }
 127         catch(exception& e) {
 128                 m->errorOut(e, "MakeBiomCommand", "getHelpString");
 129                 exit(1);
 130         }
 131 }
 132 //**********************************************************************************************************************
 133 MakeBiomCommand::MakeBiomCommand(){
 134         try {
 135                 abort = true; calledHelp = true;
 136                 setParameters();
 137                 vector<string> tempOutNames;
 138                 outputTypes["biom"] = tempOutNames;
 139         }
 140         catch(exception& e) {
 141                 m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand");
 142                 exit(1);
 143         }
 144 }
 145 //**********************************************************************************************************************
 146 MakeBiomCommand::MakeBiomCommand(string option) {
 147         try {
 148                 abort = false; calledHelp = false;
 149                 allLines = 1;
 150
 151                 //allow user to run help
 152                 if(option == "help") { help(); abort = true; calledHelp = true; }
 153                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 154
 155                 else {
 156                         vector<string> myArray = setParameters();
 157
 158                         OptionParser parser(option);
 159                         map<string,string> parameters = parser.getParameters();
 160                         map<string,string>::iterator it;
 161
 162                         ValidParameters validParameter;
 163
 164                         //check to make sure all parameters are valid for command
 165                         for (it = parameters.begin(); it != parameters.end(); it++) {
 166                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 167                         }
 168
 169                         //initialize outputTypes
 170                         vector<string> tempOutNames;
 171                         outputTypes["relabund"] = tempOutNames;
 172
 173                         //if the user changes the input directory command factory will send this info to us in the output parameter
 174                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 175                         if (inputDir == "not found"){   inputDir = "";          }
 176                         else {
 177                                 string path;
 178                                 it = parameters.find("shared");
 179                                 //user has given a template file
 180                                 if(it != parameters.end()){
 181                                         path = m->hasPath(it->second);
 182                                         //if the user has not given a path then, add inputdir. else leave path alone.
 183                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 184                                 }
 185
 186                 it = parameters.find("contaxonomy");
 187                                 //user has given a template file
 188                                 if(it != parameters.end()){
 189                                         path = m->hasPath(it->second);
 190                                         //if the user has not given a path then, add inputdir. else leave path alone.
 191                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 192                                 }
 193                         }
 194
 195                         //get shared file
 196                         sharedfile = validParameter.validFile(parameters, "shared", true);
 197                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 198                         else if (sharedfile == "not found") {
 199                                 //if there is a current shared file, use it
 200                                 sharedfile = m->getSharedFile();
 201                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 202                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 203                         }else { m->setSharedFile(sharedfile); }
 204
 205
 206                         //if the user changes the output directory command factory will send this info to us in the output parameter
 207                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 208
 209             contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 210                         if (contaxonomyfile == "not found") {  contaxonomyfile = "";  }
 211                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 212
 213
 214                         //check for optional parameter and set defaults
 215                         // ...at some point should added some additional type checking...
 216                         label = validParameter.validFile(parameters, "label", false);
 217                         if (label == "not found") { label = ""; }
 218                         else {
 219                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 220                                 else { allLines = 1;  }
 221                         }
 222
 223                         groups = validParameter.validFile(parameters, "groups", false);
 224                         if (groups == "not found") { groups = ""; }
 225                         else {
 226                                 m->splitAtDash(groups, Groups);
 227                                 m->setGroups(Groups);
 228                         }
 229
 230             if ((contaxonomyfile != "") && (labels.size() > 1)) { m->mothurOut("[ERROR]: the contaxonomy parameter cannot be used with multiple labels."); m->mothurOutEndLine(); abort = true; }
 231
 232                         format = validParameter.validFile(parameters, "matrixtype", false);                             if (format == "not found") { format = "sparse"; }
 233
 234                         if ((format != "sparse") && (format != "dense")) {
 235                                 m->mothurOut(format + " is not a valid option for the matrixtype parameter. Options are sparse and dense."); m->mothurOutEndLine(); abort = true;
 236                         }
 237                 }
 238
 239         }
 240         catch(exception& e) {
 241                 m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand");
 242                 exit(1);
 243         }
 244 }
 245 //**********************************************************************************************************************
 246
 247 int MakeBiomCommand::execute(){
 248         try {
 249
 250                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 251
 252                 InputData input(sharedfile, "sharedfile");
 253                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 254                 string lastLabel = lookup[0]->getLabel();
 255
 256         //if user did not specify a label, then use first one
 257         if ((contaxonomyfile != "") && (labels.size() == 0)) {
 258             allLines = 0;
 259             labels.insert(lastLabel);
 260         }
 261
 262                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 263                 set<string> processedLabels;
 264                 set<string> userLabels = labels;
 265
 266                 //as long as you are not at the end of the file or done wih the lines you want
 267                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 268
 269                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
 270
 271                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 272
 273                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 274                                 getBiom(lookup);
 275
 276                                 processedLabels.insert(lookup[0]->getLabel());
 277                                 userLabels.erase(lookup[0]->getLabel());
 278                         }
 279
 280                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 281                                 string saveLabel = lookup[0]->getLabel();
 282
 283                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 284                                 lookup = input.getSharedRAbundVectors(lastLabel);
 285                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 286
 287                                 getBiom(lookup);
 288
 289                                 processedLabels.insert(lookup[0]->getLabel());
 290                                 userLabels.erase(lookup[0]->getLabel());
 291
 292                                 //restore real lastlabel to save below
 293                                 lookup[0]->setLabel(saveLabel);
 294                         }
 295
 296                         lastLabel = lookup[0]->getLabel();
 297
 298                         //prevent memory leak and get next set
 299                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 300                         lookup = input.getSharedRAbundVectors();
 301                 }
 302
 303         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 304
 305                 //output error messages about any remaining user labels
 306                 set<string>::iterator it;
 307                 bool needToRun = false;
 308                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 309                         m->mothurOut("Your file does not include the label " + *it);
 310                         if (processedLabels.count(lastLabel) != 1) {
 311                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 312                                 needToRun = true;
 313                         }else {
 314                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 315                         }
 316                 }
 317
 318                 //run last label if you need to
 319                 if (needToRun == true)  {
 320                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 321                         lookup = input.getSharedRAbundVectors(lastLabel);
 322
 323                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 324             getBiom(lookup);
 325
 326                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 327                 }
 328
 329         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 330
 331                 m->mothurOutEndLine();
 332                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 333                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 334                 m->mothurOutEndLine();
 335
 336                 return 0;
 337         }
 338         catch(exception& e) {
 339                 m->errorOut(e, "MakeBiomCommand", "execute");
 340                 exit(1);
 341         }
 342 }
 343 //**********************************************************************************************************************
 344 int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
 345         try {
 346
 347         string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".biom";
 348                 ofstream out;
 349                 m->openOutputFile(outputFileName, out);
 350                 outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
 351
 352         string mothurString = "mothur" + toString(m->getVersion());
 353         time_t rawtime;
 354         struct tm * timeinfo;
 355         time ( &rawtime );
 356         timeinfo = localtime ( &rawtime );
 357         string dateString = asctime (timeinfo);
 358         int pos = dateString.find('\n');
 359         if (pos != string::npos) { dateString = dateString.substr(0, pos);}
 360         string spaces = "      ";
 361
 362         //standard
 363         out << "{\n" + spaces + "\"id\":\"" + sharedfile + "-" + lookup[0]->getLabel() + "\",\n" + spaces + "\"format\": \"Biological Observation Matrix 0.9.1\",\n" + spaces + "\"format_url\": \"http://biom-format.org\",\n";
 364         out << spaces + "\"type\": \"OTU table\",\n" + spaces + "\"generated_by\": \"" << mothurString << "\",\n" + spaces + "\"date\": \"" << dateString << "\",\n";
 365
 366         vector<string> metadata = getMetaData(lookup);
 367
 368         if (m->control_pressed) {  out.close(); return 0; }
 369
 370         //get row info
 371         /*"rows":[
 372                 {"id":"GG_OTU_1", "metadata":null},
 373                 {"id":"GG_OTU_2", "metadata":null},
 374                 {"id":"GG_OTU_3", "metadata":null},
 375                 {"id":"GG_OTU_4", "metadata":null},
 376                 {"id":"GG_OTU_5", "metadata":null}
 377                 ],*/
 378         out << spaces + "\"rows\":[\n";
 379         string rowFront = spaces + spaces + "{\"id\":\"";
 380         string rowBack = "\", \"metadata\":";
 381         for (int i = 0; i < m->currentBinLabels.size()-1; i++) {
 382             if (m->control_pressed) {  out.close(); return 0; }
 383             out << rowFront << m->currentBinLabels[i] << rowBack << metadata[i] << "},\n";
 384         }
 385         out << rowFront << m->currentBinLabels[(m->currentBinLabels.size()-1)] << rowBack << metadata[(m->currentBinLabels.size()-1)] << "}\n" + spaces + "],\n";
 386
 387         //get column info
 388         /*"columns": [
 389                     {"id":"Sample1", "metadata":null},
 390                     {"id":"Sample2", "metadata":null},
 391                     {"id":"Sample3", "metadata":null},
 392                     {"id":"Sample4", "metadata":null},
 393                     {"id":"Sample5", "metadata":null},
 394                     {"id":"Sample6", "metadata":null}
 395                     ],*/
 396
 397         string colBack = "\", \"metadata\":null}";
 398         out << spaces + "\"columns\":[\n";
 399         for (int i = 0; i < lookup.size()-1; i++) {
 400             if (m->control_pressed) {  out.close(); return 0; }
 401             out << rowFront << lookup[i]->getGroup() << colBack << ",\n";
 402         }
 403         out << rowFront << lookup[(lookup.size()-1)]->getGroup() << colBack << "\n" + spaces + "],\n";
 404
 405         out << spaces + "\"matrix_type\": \"" << format << "\",\n" + spaces + "\"matrix_element_type\": \"int\",\n";
 406         out <<  spaces + "\"shape\": [" << m->currentBinLabels.size() << "," << lookup.size() << "],\n";
 407         out << spaces + "\"data\":  [";
 408
 409         vector<string> dataRows;
 410         if (format == "sparse") {
 411             /*"data":[[0,2,1],
 412              [1,0,5],
 413              [1,1,1],
 414              [1,3,2],
 415              [1,4,3],
 416              [1,5,1],
 417              [2,2,1],
 418              [2,3,4],
 419              [2,4,2],
 420              [3,0,2],
 421              [3,1,1],
 422              [3,2,1],
 423              [3,5,1],
 424              [4,1,1],
 425              [4,2,1]
 426              ]*/
 427             string output = "";
 428             for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 429
 430                 if (m->control_pressed) { out.close(); return 0; }
 431
 432                 for (int j = 0; j < lookup.size(); j++) {
 433                     string binInfo = "[" + toString(i) + "," + toString(j) + "," + toString(lookup[j]->getAbundance(i)) + "]";
 434                     //only print non zero values
 435                     if (lookup[j]->getAbundance(i) != 0) { dataRows.push_back(binInfo); }
 436                 }
 437             }
 438         }else {
 439
 440             /* "matrix_type": "dense",
 441              "matrix_element_type": "int",
 442              "shape": [5,6],
 443              "data":  [[0,0,1,0,0,0],
 444              [5,1,0,2,3,1],
 445              [0,0,1,4,2,0],
 446              [2,1,1,0,0,1],
 447              [0,1,1,0,0,0]]*/
 448
 449             for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 450
 451                 if (m->control_pressed) { out.close(); return 0; }
 452
 453                 string binInfo = "[";
 454                 for (int j = 0; j < lookup.size()-1; j++) {
 455                     binInfo += toString(lookup[j]->getAbundance(i)) + ",";
 456                 }
 457                 binInfo += toString(lookup[lookup.size()-1]->getAbundance(i)) + "]";
 458                 dataRows.push_back(binInfo);
 459             }
 460         }
 461
 462         for (int i = 0; i < dataRows.size()-1; i++) {
 463             out << dataRows[i] << ",\n" + spaces  + spaces;
 464         }
 465         out << dataRows[dataRows.size()-1] << "]\n";
 466
 467         out << "}\n";
 468         out.close();
 469
 470         return 0;
 471     }
 472         catch(exception& e) {
 473                 m->errorOut(e, "MakeBiomCommand", "getBiom");
 474                 exit(1);
 475         }
 476 }
 477 //**********************************************************************************************************************
 478 vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup){
 479         try {
 480         vector<string> metadata;
 481
 482         if (contaxonomyfile == "") { for (int i = 0; i < lookup[0]->getNumBins(); i++) {  metadata.push_back("null");  } }
 483         else {
 484
 485             //read constaxonomy file storing in a map, otulabel -> taxonomy
 486             //constaxonomy file will most likely contain more labels than the shared file, because sharedfile could have been subsampled.
 487             ifstream in;
 488             m->openInputFile(contaxonomyfile, in);
 489
 490             //grab headers
 491             m->getline(in); m->gobble(in);
 492
 493             string otuLabel, tax;
 494             int size;
 495             vector<string> otuLabels;
 496             vector<string> taxs;
 497             while (!in.eof()) {
 498
 499                 if (m->control_pressed) { in.close(); return metadata; }
 500
 501                 in >> otuLabel >> size >> tax; m->gobble(in);
 502
 503                 otuLabels.push_back(otuLabel);
 504                 taxs.push_back(tax);
 505             }
 506             in.close();
 507
 508             //should the labels be Otu001 or PhyloType001
 509             string firstBin = m->currentBinLabels[0];
 510             string binTag = "Otu";
 511             if ((firstBin.find("Otu")) == string::npos) { binTag = "PhyloType";  }
 512
 513             //convert list file bin labels to shared file bin labels
 514             //parse tax strings
 515             //save in map
 516             map<string, vector<string> > labelTaxMap;
 517             string snumBins = toString(otuLabels.size());
 518             for (int i = 0; i < otuLabels.size(); i++) {
 519
 520                 if (m->control_pressed) { return metadata; }
 521
 522                 //if there is a bin label use it otherwise make one
 523                 string binLabel = binTag;
 524                 string sbinNumber = otuLabels[i];
 525                 if (sbinNumber.length() < snumBins.length()) {
 526                     int diff = snumBins.length() - sbinNumber.length();
 527                     for (int h = 0; h < diff; h++) { binLabel += "0"; }
 528                 }
 529                 binLabel += sbinNumber;
 530
 531                 vector<string> taxString;
 532                 m->splitAtChar(taxs[i], taxString, ';');
 533                 taxString.pop_back(); //adds blank string because taxonomies end in ;
 534
 535                 labelTaxMap[binLabel] = taxString;
 536             }
 537
 538
 539             //{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}
 540
 541             //traverse the binLabels forming the metadata strings and saving them
 542             //make sure to sanity check
 543             map<string, vector<string> >::iterator it;
 544             for (int i = 0; i < m->currentBinLabels.size(); i++) {
 545
 546                 if (m->control_pressed) { return metadata; }
 547
 548                 it = labelTaxMap.find(m->currentBinLabels[i]);
 549
 550                 if (it == labelTaxMap.end()) { m->mothurOut("[ERROR]: can't find taxonomy information for " + m->currentBinLabels[i] + ".\n"); m->control_pressed = true; }
 551                 else {
 552                     string data = "{\"taxonomy\":[";
 553                     for (int j = 0; j < (it->second).size()-1; j ++) {
 554
 555                         string taxon = (it->second)[j];
 556
 557                         //strip "" if they are there
 558                         int pos = taxon.find("\"");
 559                         if (pos != string::npos) {
 560                             string newTax = "";
 561                             for (int k = 0; k < taxon.length(); k++) {
 562                                 if (taxon[k] != '\"') { newTax += taxon[k]; }
 563                             }
 564                             taxon = newTax;
 565                         }
 566
 567                         data += "\"" + taxon + "\", ";
 568                     }
 569
 570                     string taxon = (it->second)[(it->second).size()-1];
 571
 572                     //strip "" if they are there
 573                     int pos = taxon.find("\"");
 574                     if (pos != string::npos) {
 575                         string newTax = "";
 576                         for (int k = 0; k < taxon.length(); k++) {
 577                             if (taxon[k] != '\"') { newTax += taxon[k]; }
 578                         }
 579                         taxon = newTax;
 580                     }
 581
 582                     data += "\"" + taxon + "\"]} ";
 583
 584                     metadata.push_back(data);
 585                 }
 586             }
 587         }
 588
 589         return metadata;
 590
 591     }
 592         catch(exception& e) {
 593                 m->errorOut(e, "MakeBiomCommand", "getMetadata");
 594                 exit(1);
 595         }
 596
 597 }
 598 //**********************************************************************************************************************
 599
 600
 601