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, contaxonomy, 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 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.\n";
 120                 helpString += "The make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\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 string MakeBiomCommand::getOutputFileNameTag(string type, string inputName=""){
 134         try {
 135         string outputFileName = "";
 136                 map<string, vector<string> >::iterator it;
 137
 138         //is this a type this command creates
 139         it = outputTypes.find(type);
 140         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
 141         else {
 142             if (type == "biom")             {   outputFileName =  "biom";       }
 143             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 144         }
 145         return outputFileName;
 146         }
 147         catch(exception& e) {
 148                 m->errorOut(e, "MakeBiomCommand", "getOutputFileNameTag");
 149                 exit(1);
 150         }
 151 }
 152
 153 //**********************************************************************************************************************
 154 MakeBiomCommand::MakeBiomCommand(){
 155         try {
 156                 abort = true; calledHelp = true;
 157                 setParameters();
 158                 vector<string> tempOutNames;
 159                 outputTypes["biom"] = tempOutNames;
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand");
 163                 exit(1);
 164         }
 165 }
 166 //**********************************************************************************************************************
 167 MakeBiomCommand::MakeBiomCommand(string option) {
 168         try {
 169                 abort = false; calledHelp = false;
 170                 allLines = 1;
 171
 172                 //allow user to run help
 173                 if(option == "help") { help(); abort = true; calledHelp = true; }
 174                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 175
 176                 else {
 177                         vector<string> myArray = setParameters();
 178
 179                         OptionParser parser(option);
 180                         map<string,string> parameters = parser.getParameters();
 181                         map<string,string>::iterator it;
 182
 183                         ValidParameters validParameter;
 184
 185                         //check to make sure all parameters are valid for command
 186                         for (it = parameters.begin(); it != parameters.end(); it++) {
 187                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 188                         }
 189
 190                         //initialize outputTypes
 191                         vector<string> tempOutNames;
 192                         outputTypes["biom"] = tempOutNames;
 193
 194                         //if the user changes the input directory command factory will send this info to us in the output parameter
 195                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 196                         if (inputDir == "not found"){   inputDir = "";          }
 197                         else {
 198                                 string path;
 199                                 it = parameters.find("shared");
 200                                 //user has given a template file
 201                                 if(it != parameters.end()){
 202                                         path = m->hasPath(it->second);
 203                                         //if the user has not given a path then, add inputdir. else leave path alone.
 204                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 205                                 }
 206
 207                 it = parameters.find("contaxonomy");
 208                                 //user has given a template file
 209                                 if(it != parameters.end()){
 210                                         path = m->hasPath(it->second);
 211                                         //if the user has not given a path then, add inputdir. else leave path alone.
 212                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 213                                 }
 214                         }
 215
 216                         //get shared file
 217                         sharedfile = validParameter.validFile(parameters, "shared", true);
 218                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 219                         else if (sharedfile == "not found") {
 220                                 //if there is a current shared file, use it
 221                                 sharedfile = m->getSharedFile();
 222                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 223                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 224                         }else { m->setSharedFile(sharedfile); }
 225
 226
 227                         //if the user changes the output directory command factory will send this info to us in the output parameter
 228                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 229
 230             contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 231                         if (contaxonomyfile == "not found") {  contaxonomyfile = "";  }
 232                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 233
 234
 235                         //check for optional parameter and set defaults
 236                         // ...at some point should added some additional type checking...
 237                         label = validParameter.validFile(parameters, "label", false);
 238                         if (label == "not found") { label = ""; }
 239                         else {
 240                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 241                                 else { allLines = 1;  }
 242                         }
 243
 244                         groups = validParameter.validFile(parameters, "groups", false);
 245                         if (groups == "not found") { groups = ""; }
 246                         else {
 247                                 m->splitAtDash(groups, Groups);
 248                                 m->setGroups(Groups);
 249                         }
 250
 251             if ((contaxonomyfile != "") && (labels.size() > 1)) { m->mothurOut("[ERROR]: the contaxonomy parameter cannot be used with multiple labels."); m->mothurOutEndLine(); abort = true; }
 252
 253                         format = validParameter.validFile(parameters, "matrixtype", false);                             if (format == "not found") { format = "sparse"; }
 254
 255                         if ((format != "sparse") && (format != "dense")) {
 256                                 m->mothurOut(format + " is not a valid option for the matrixtype parameter. Options are sparse and dense."); m->mothurOutEndLine(); abort = true;
 257                         }
 258                 }
 259
 260         }
 261         catch(exception& e) {
 262                 m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand");
 263                 exit(1);
 264         }
 265 }
 266 //**********************************************************************************************************************
 267
 268 int MakeBiomCommand::execute(){
 269         try {
 270
 271                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 272
 273                 InputData input(sharedfile, "sharedfile");
 274                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 275                 string lastLabel = lookup[0]->getLabel();
 276
 277         //if user did not specify a label, then use first one
 278         if ((contaxonomyfile != "") && (labels.size() == 0)) {
 279             allLines = 0;
 280             labels.insert(lastLabel);
 281         }
 282
 283                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 284                 set<string> processedLabels;
 285                 set<string> userLabels = labels;
 286
 287                 //as long as you are not at the end of the file or done wih the lines you want
 288                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 289
 290                         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; }
 291
 292                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 293
 294                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 295                                 getBiom(lookup);
 296
 297                                 processedLabels.insert(lookup[0]->getLabel());
 298                                 userLabels.erase(lookup[0]->getLabel());
 299                         }
 300
 301                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 302                                 string saveLabel = lookup[0]->getLabel();
 303
 304                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 305                                 lookup = input.getSharedRAbundVectors(lastLabel);
 306                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 307
 308                                 getBiom(lookup);
 309
 310                                 processedLabels.insert(lookup[0]->getLabel());
 311                                 userLabels.erase(lookup[0]->getLabel());
 312
 313                                 //restore real lastlabel to save below
 314                                 lookup[0]->setLabel(saveLabel);
 315                         }
 316
 317                         lastLabel = lookup[0]->getLabel();
 318
 319                         //prevent memory leak and get next set
 320                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 321                         lookup = input.getSharedRAbundVectors();
 322                 }
 323
 324         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 325
 326                 //output error messages about any remaining user labels
 327                 set<string>::iterator it;
 328                 bool needToRun = false;
 329                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 330                         m->mothurOut("Your file does not include the label " + *it);
 331                         if (processedLabels.count(lastLabel) != 1) {
 332                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 333                                 needToRun = true;
 334                         }else {
 335                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 336                         }
 337                 }
 338
 339                 //run last label if you need to
 340                 if (needToRun == true)  {
 341                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 342                         lookup = input.getSharedRAbundVectors(lastLabel);
 343
 344                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 345             getBiom(lookup);
 346
 347                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 348                 }
 349
 350         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 351
 352         //set sabund file as new current sabundfile
 353         string current = "";
 354                 itTypes = outputTypes.find("biom");
 355                 if (itTypes != outputTypes.end()) {
 356                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setBiomFile(current); }
 357                 }
 358
 359
 360                 m->mothurOutEndLine();
 361                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 362                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 363                 m->mothurOutEndLine();
 364
 365                 return 0;
 366         }
 367         catch(exception& e) {
 368                 m->errorOut(e, "MakeBiomCommand", "execute");
 369                 exit(1);
 370         }
 371 }
 372 //**********************************************************************************************************************
 373 int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
 374         try {
 375
 376         string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
 377                 ofstream out;
 378                 m->openOutputFile(outputFileName, out);
 379                 outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
 380
 381         string mothurString = "mothur" + toString(m->getVersion());
 382         time_t rawtime;
 383         struct tm * timeinfo;
 384         time ( &rawtime );
 385         timeinfo = localtime ( &rawtime );
 386         string dateString = asctime (timeinfo);
 387         int pos = dateString.find('\n');
 388         if (pos != string::npos) { dateString = dateString.substr(0, pos);}
 389         string spaces = "      ";
 390
 391         //standard
 392         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";
 393         out << spaces + "\"type\": \"OTU table\",\n" + spaces + "\"generated_by\": \"" << mothurString << "\",\n" + spaces + "\"date\": \"" << dateString << "\",\n";
 394
 395         vector<string> metadata = getMetaData(lookup);
 396
 397         if (m->control_pressed) {  out.close(); return 0; }
 398
 399         //get row info
 400         /*"rows":[
 401                 {"id":"GG_OTU_1", "metadata":null},
 402                 {"id":"GG_OTU_2", "metadata":null},
 403                 {"id":"GG_OTU_3", "metadata":null},
 404                 {"id":"GG_OTU_4", "metadata":null},
 405                 {"id":"GG_OTU_5", "metadata":null}
 406                 ],*/
 407         out << spaces + "\"rows\":[\n";
 408         string rowFront = spaces + spaces + "{\"id\":\"";
 409         string rowBack = "\", \"metadata\":";
 410         for (int i = 0; i < m->currentBinLabels.size()-1; i++) {
 411             if (m->control_pressed) {  out.close(); return 0; }
 412             out << rowFront << m->currentBinLabels[i] << rowBack << metadata[i] << "},\n";
 413         }
 414         out << rowFront << m->currentBinLabels[(m->currentBinLabels.size()-1)] << rowBack << metadata[(m->currentBinLabels.size()-1)] << "}\n" + spaces + "],\n";
 415
 416         //get column info
 417         /*"columns": [
 418                     {"id":"Sample1", "metadata":null},
 419                     {"id":"Sample2", "metadata":null},
 420                     {"id":"Sample3", "metadata":null},
 421                     {"id":"Sample4", "metadata":null},
 422                     {"id":"Sample5", "metadata":null},
 423                     {"id":"Sample6", "metadata":null}
 424                     ],*/
 425
 426         string colBack = "\", \"metadata\":null}";
 427         out << spaces + "\"columns\":[\n";
 428         for (int i = 0; i < lookup.size()-1; i++) {
 429             if (m->control_pressed) {  out.close(); return 0; }
 430             out << rowFront << lookup[i]->getGroup() << colBack << ",\n";
 431         }
 432         out << rowFront << lookup[(lookup.size()-1)]->getGroup() << colBack << "\n" + spaces + "],\n";
 433
 434         out << spaces + "\"matrix_type\": \"" << format << "\",\n" + spaces + "\"matrix_element_type\": \"int\",\n";
 435         out <<  spaces + "\"shape\": [" << m->currentBinLabels.size() << "," << lookup.size() << "],\n";
 436         out << spaces + "\"data\":  [";
 437
 438         vector<string> dataRows;
 439         if (format == "sparse") {
 440             /*"data":[[0,2,1],
 441              [1,0,5],
 442              [1,1,1],
 443              [1,3,2],
 444              [1,4,3],
 445              [1,5,1],
 446              [2,2,1],
 447              [2,3,4],
 448              [2,4,2],
 449              [3,0,2],
 450              [3,1,1],
 451              [3,2,1],
 452              [3,5,1],
 453              [4,1,1],
 454              [4,2,1]
 455              ]*/
 456             string output = "";
 457             for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 458
 459                 if (m->control_pressed) { out.close(); return 0; }
 460
 461                 for (int j = 0; j < lookup.size(); j++) {
 462                     string binInfo = "[" + toString(i) + "," + toString(j) + "," + toString(lookup[j]->getAbundance(i)) + "]";
 463                     //only print non zero values
 464                     if (lookup[j]->getAbundance(i) != 0) { dataRows.push_back(binInfo); }
 465                 }
 466             }
 467         }else {
 468
 469             /* "matrix_type": "dense",
 470              "matrix_element_type": "int",
 471              "shape": [5,6],
 472              "data":  [[0,0,1,0,0,0],
 473              [5,1,0,2,3,1],
 474              [0,0,1,4,2,0],
 475              [2,1,1,0,0,1],
 476              [0,1,1,0,0,0]]*/
 477
 478             for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 479
 480                 if (m->control_pressed) { out.close(); return 0; }
 481
 482                 string binInfo = "[";
 483                 for (int j = 0; j < lookup.size()-1; j++) {
 484                     binInfo += toString(lookup[j]->getAbundance(i)) + ",";
 485                 }
 486                 binInfo += toString(lookup[lookup.size()-1]->getAbundance(i)) + "]";
 487                 dataRows.push_back(binInfo);
 488             }
 489         }
 490
 491         for (int i = 0; i < dataRows.size()-1; i++) {
 492             out << dataRows[i] << ",\n" + spaces  + spaces;
 493         }
 494         out << dataRows[dataRows.size()-1] << "]\n";
 495
 496         out << "}\n";
 497         out.close();
 498
 499         return 0;
 500     }
 501         catch(exception& e) {
 502                 m->errorOut(e, "MakeBiomCommand", "getBiom");
 503                 exit(1);
 504         }
 505 }
 506 //**********************************************************************************************************************
 507 vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup){
 508         try {
 509         vector<string> metadata;
 510
 511         if (contaxonomyfile == "") { for (int i = 0; i < lookup[0]->getNumBins(); i++) {  metadata.push_back("null");  } }
 512         else {
 513
 514             //read constaxonomy file storing in a map, otulabel -> taxonomy
 515             //constaxonomy file will most likely contain more labels than the shared file, because sharedfile could have been subsampled.
 516             ifstream in;
 517             m->openInputFile(contaxonomyfile, in);
 518
 519             //grab headers
 520             m->getline(in); m->gobble(in);
 521
 522             string otuLabel, tax;
 523             int size;
 524             vector<string> otuLabels;
 525             vector<string> taxs;
 526             while (!in.eof()) {
 527
 528                 if (m->control_pressed) { in.close(); return metadata; }
 529
 530                 in >> otuLabel >> size >> tax; m->gobble(in);
 531
 532                 otuLabels.push_back(otuLabel);
 533                 taxs.push_back(tax);
 534             }
 535             in.close();
 536
 537             //should the labels be Otu001 or PhyloType001
 538             string firstBin = m->currentBinLabels[0];
 539             string binTag = "Otu";
 540             if ((firstBin.find("Otu")) == string::npos) { binTag = "PhyloType";  }
 541
 542             //convert list file bin labels to shared file bin labels
 543             //parse tax strings
 544             //save in map
 545             map<string, string> labelTaxMap;
 546             string snumBins = toString(otuLabels.size());
 547             for (int i = 0; i < otuLabels.size(); i++) {
 548
 549                 if (m->control_pressed) { return metadata; }
 550
 551                 //if there is a bin label use it otherwise make one
 552                 if (m->isContainingOnlyDigits(otuLabels[i])) {
 553                     string binLabel = binTag;
 554                     string sbinNumber = otuLabels[i];
 555                     if (sbinNumber.length() < snumBins.length()) {
 556                         int diff = snumBins.length() - sbinNumber.length();
 557                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 558                     }
 559                     binLabel += sbinNumber;
 560                     labelTaxMap[binLabel] = taxs[i];
 561                 }else {  labelTaxMap[otuLabels[i]] = taxs[i]; }
 562             }
 563
 564
 565             //{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}
 566
 567             //traverse the binLabels forming the metadata strings and saving them
 568             //make sure to sanity check
 569             map<string, string>::iterator it;
 570             for (int i = 0; i < m->currentBinLabels.size(); i++) {
 571
 572                 if (m->control_pressed) { return metadata; }
 573
 574                 it = labelTaxMap.find(m->currentBinLabels[i]);
 575
 576                 if (it == labelTaxMap.end()) { m->mothurOut("[ERROR]: can't find taxonomy information for " + m->currentBinLabels[i] + ".\n"); m->control_pressed = true; }
 577                 else {
 578                     vector<string> bootstrapValues;
 579                     string data = "{\"taxonomy\":[";
 580
 581                     vector<string> scores;
 582                     vector<string> taxonomies = parseTax(it->second, scores);
 583
 584                     for (int j = 0; j < taxonomies.size()-1; j ++) { data += "\"" + taxonomies[j] + "\", "; }
 585                     data += "\"" + taxonomies[taxonomies.size()-1] + "\"]";
 586
 587                     //add bootstrap values if available
 588                     if (scores[0] != "null") {
 589                         data += ", \"bootstrap\":[";
 590
 591                         for (int j = 0; j < scores.size()-1; j ++) { data += scores[j] + ", "; }
 592                         data += scores[scores.size()-1] + "]";
 593
 594                     }
 595                     data += "}";
 596
 597                     metadata.push_back(data);
 598                 }
 599             }
 600         }
 601
 602         return metadata;
 603
 604     }
 605         catch(exception& e) {
 606                 m->errorOut(e, "MakeBiomCommand", "getMetadata");
 607                 exit(1);
 608         }
 609
 610 }
 611 /**************************************************************************************************/
 612 //returns {Bacteria, Bacteroidetes, ..} and scores is filled with {100, 98, ...} or {null, null, null}
 613 vector<string> MakeBiomCommand::parseTax(string tax, vector<string>& scores) {
 614         try {
 615
 616                 string taxon;
 617         vector<string> taxs;
 618
 619                 while (tax.find_first_of(';') != -1) {
 620
 621                         if (m->control_pressed) { return taxs; }
 622
 623                         //get taxon
 624                         taxon = tax.substr(0,tax.find_first_of(';'));
 625
 626                         int pos = taxon.find_last_of('(');
 627                         if (pos != -1) {
 628                                 //is it a number?
 629                                 int pos2 = taxon.find_last_of(')');
 630                                 if (pos2 != -1) {
 631                                         string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
 632                                         if (m->isNumeric1(confidenceScore)) {
 633                                                 taxon = taxon.substr(0, pos); //rip off confidence
 634                         scores.push_back(confidenceScore);
 635                                         }else{ scores.push_back("null"); }
 636                                 }
 637                         }else{ scores.push_back("null"); }
 638
 639             //strip "" if they are there
 640             pos = taxon.find("\"");
 641             if (pos != string::npos) {
 642                 string newTax = "";
 643                 for (int k = 0; k < taxon.length(); k++) {
 644                     if (taxon[k] != '\"') { newTax += taxon[k]; }
 645                 }
 646                 taxon = newTax;
 647             }
 648
 649             //look for bootstrap value
 650                         taxs.push_back(taxon);
 651             tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 652                 }
 653
 654                 return taxs;
 655         }
 656         catch(exception& e) {
 657                 m->errorOut(e, "MakeBiomCommand", "parseTax");
 658                 exit(1);
 659         }
 660 }
 661
 662 //**********************************************************************************************************************
 663
 664
 665