createdatabasecommand.cpp

   1 //
   2 //  createdatabasecommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 3/28/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "createdatabasecommand.h"
  10 #include "inputdata.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> CreateDatabaseCommand::setParameters(){
  14         try {
  15                 CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,true,true); parameters.push_back(pfasta);
  16                 CommandParameter pname("repname", "InputTypes", "", "", "NameCount", "NameCount", "none","",false,false,true); parameters.push_back(pname);
  17         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none","",false,false,true); parameters.push_back(pcount);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  19                 CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pcontaxonomy);
  20                 CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(plist);
  21         CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(pshared);
  22                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "CreateDatabaseCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string CreateDatabaseCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The create.database command reads a list file or a shared file, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, or count file and creates a database file.\n";
  40                 helpString += "The create.database command parameters are repfasta, list, shared, repname, contaxonomy, group, count and label. List, repfasta, repnames or count, and contaxonomy are required.\n";
  41         helpString += "The repfasta file is fasta file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
  42         helpString += "The repname file is the name file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
  43         helpString += "The count file is the count file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, count=yourCountFile). If it includes group info, mothur will give you the abundance breakdown by group. \n";
  44         helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile, name=yourNameFile).\n";
  45         helpString += "The group file is optional and will just give you the abundance breakdown by group.\n";
  46         helpString += "The label parameter allows you to specify a label to be used from your listfile.\n";
  47         helpString += "NOTE: Make SURE the repfasta, repnames and contaxonomy are for the same label as the listfile.\n";
  48         helpString += "The create.database command should be in the following format: \n";
  49                 helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
  50                 helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, repname=final.an.0.03.rep.names, list=final.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 string CreateDatabaseCommand::getOutputPattern(string type) {
  61     try {
  62         string pattern = "";
  63
  64         if (type == "database") {  pattern = "[filename],database"; }
  65         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  66
  67         return pattern;
  68     }
  69     catch(exception& e) {
  70         m->errorOut(e, "CreateDatabaseCommand", "getOutputPattern");
  71         exit(1);
  72     }
  73 }
  74 //**********************************************************************************************************************
  75 CreateDatabaseCommand::CreateDatabaseCommand(){
  76         try {
  77                 abort = true; calledHelp = true;
  78                 setParameters();
  79                 vector<string> tempOutNames;
  80                 outputTypes["database"] = tempOutNames;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
  84                 exit(1);
  85         }
  86 }
  87
  88 //**********************************************************************************************************************
  89 CreateDatabaseCommand::CreateDatabaseCommand(string option)  {
  90         try{
  91                 abort = false; calledHelp = false;
  92
  93                 //allow user to run help
  94                 if (option == "help") {
  95                         help(); abort = true; calledHelp = true;
  96                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  97                 else {
  98                         vector<string> myArray = setParameters();
  99
 100                         OptionParser parser(option);
 101                         map<string, string> parameters = parser.getParameters();
 102
 103                         ValidParameters validParameter;
 104                         map<string, string>::iterator it;
 105
 106                         //check to make sure all parameters are valid for command
 107                         for (it = parameters.begin(); it != parameters.end(); it++) {
 108                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 109                         }
 110
 111                         //initialize outputTypes
 112                         vector<string> tempOutNames;
 113                         outputTypes["database"] = tempOutNames;
 114
 115                         //if the user changes the input directory command factory will send this info to us in the output parameter
 116                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 117                         if (inputDir == "not found"){   inputDir = "";          }
 118                         else {
 119                                 string path;
 120                                 it = parameters.find("list");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 126                                 }
 127
 128                                 it = parameters.find("repname");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["repname"] = inputDir + it->second;          }
 134                                 }
 135
 136                                 it = parameters.find("contaxonomy");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 142                                 }
 143
 144                                 it = parameters.find("repfasta");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["repfasta"] = inputDir + it->second;         }
 150                                 }
 151
 152                                 it = parameters.find("group");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 158                                 }
 159
 160                 it = parameters.find("count");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 166                                 }
 167
 168                 it = parameters.find("shared");
 169                                 //user has given a template file
 170                                 if(it != parameters.end()){
 171                                         path = m->hasPath(it->second);
 172                                         //if the user has not given a path then, add inputdir. else leave path alone.
 173                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 174                                 }
 175                         }
 176
 177
 178                         //if the user changes the output directory command factory will send this info to us in the output parameter
 179                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 180
 181                         //check for required parameters
 182                         listfile = validParameter.validFile(parameters, "list", true);
 183                         if (listfile == "not found") {  listfile = "";                  }
 184                         else if (listfile == "not open") { listfile = ""; abort = true; }
 185                         else { m->setListFile(listfile); }
 186
 187             sharedfile = validParameter.validFile(parameters, "shared", true);
 188                         if (sharedfile == "not found") {        sharedfile = "";                        }
 189                         else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 190                         else { m->setSharedFile(sharedfile); }
 191
 192             if ((sharedfile == "") && (listfile == "")) {
 193                                 //is there are current file available for either of these?
 194                                 //give priority to list, then shared
 195                                 listfile = m->getListFile();
 196                                 if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 197                                 else {
 198                                         sharedfile = m->getSharedFile();
 199                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 200                                         else {
 201                                                 m->mothurOut("No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
 202                                                 abort = true;
 203                                         }
 204                                 }
 205                         }
 206                         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; }
 207
 208             if (sharedfile != "") { if (outputDir == "") { outputDir = m->hasPath(sharedfile); } }
 209             else { if (outputDir == "") { outputDir = m->hasPath(listfile); } }
 210
 211                         contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 212                         if (contaxonomyfile == "not found") {  //if there is a current list file, use it
 213                contaxonomyfile = "";  m->mothurOut("The contaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 214                         }
 215                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 216
 217             repfastafile = validParameter.validFile(parameters, "repfasta", true);
 218                         if (repfastafile == "not found") {  //if there is a current list file, use it
 219                 repfastafile = "";  m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 220                         }
 221                         else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
 222
 223             repnamesfile = validParameter.validFile(parameters, "repname", true);
 224                         if (repnamesfile == "not found") {  repnamesfile = "";                          }
 225                         else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
 226
 227             countfile = validParameter.validFile(parameters, "count", true);
 228                         if (countfile == "not found") {  countfile = "";                        }
 229                         else if (countfile == "not open") { countfile = ""; abort = true; }
 230
 231             if ((countfile == "") && (repnamesfile == "")) {
 232                 //if there is a current name file, use it, else look for current count file
 233                 string repnamesfile = m->getNameFile();
 234                                 if (repnamesfile != "") {  m->mothurOut("Using " + repnamesfile + " as input file for the repname parameter."); m->mothurOutEndLine(); }
 235                                 else {
 236                     countfile = m->getCountTableFile();
 237                     if (countfile != "") {  m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 238                     else { m->mothurOut("[ERROR]: You must provide a count or repname file."); m->mothurOutEndLine(); abort = true;  }
 239                 }
 240             }
 241
 242                         groupfile = validParameter.validFile(parameters, "group", true);
 243                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 244                         else if (groupfile == "not found") { groupfile = ""; }
 245                         else { m->setGroupFile(groupfile); }
 246
 247                         //check for optional parameter and set defaults
 248                         // ...at some point should added some additional type checking...
 249             label = validParameter.validFile(parameters, "label", false);
 250                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
 251         }
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
 255                 exit(1);
 256         }
 257 }
 258 //**********************************************************************************************************************
 259 int CreateDatabaseCommand::execute(){
 260         try {
 261
 262                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 263
 264         //taxonomies holds the taxonomy info for each Otu
 265         //classifyOtuSizes holds the size info of each Otu to help with error checking
 266         vector<string> taxonomies;
 267         vector<string> otuLabels;
 268         vector<int> classifyOtuSizes = readTax(taxonomies, otuLabels);
 269
 270         if (m->control_pressed) { return 0; }
 271
 272         vector<Sequence> seqs;
 273         vector<int> repOtusSizes = readFasta(seqs);
 274
 275         if (m->control_pressed) { return 0; }
 276
 277         //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.
 278         map<string, string> repNames;
 279         map<string, int> nameMap;
 280         int numUniqueNamesFile = 0;
 281         CountTable ct;
 282         if (countfile == "") {
 283             numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
 284             //the repnames file does not have the same order as the list file bins so we need to sort and reassemble for the search below
 285             map<string, string> tempRepNames;
 286             for (map<string, string>::iterator it = repNames.begin(); it != repNames.end();) {
 287                 string bin = it->first;
 288                 vector<string> temp;
 289                 m->splitAtChar(bin, temp, ',');
 290                 sort(temp.begin(), temp.end());
 291                 bin = "";
 292                 for (int i = 0; i < temp.size()-1; i++) {
 293                     bin += temp[i] + ',';
 294                 }
 295                 bin += temp[temp.size()-1];
 296                 tempRepNames[bin] = it->second;
 297                 repNames.erase(it++);
 298             }
 299             repNames = tempRepNames;
 300         }else {
 301             ct.readTable(countfile, true);
 302             numUniqueNamesFile = ct.getNumUniqueSeqs();
 303             nameMap = ct.getNameMap();
 304         }
 305
 306         //are there the same number of otus in the fasta and name files
 307         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; }
 308
 309         if (m->control_pressed) { return 0; }
 310
 311         //are there the same number of OTUs in the tax and fasta file
 312         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; }
 313
 314         if (m->control_pressed) { return 0; }
 315
 316         //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
 317         for (int i = 0; i < classifyOtuSizes.size(); i++) {
 318             if (classifyOtuSizes[i] != repOtusSizes[i]) {
 319                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;
 320             }
 321         }
 322
 323         if (m->control_pressed) { return 0; }
 324
 325
 326         map<string, string> variables;
 327         if (listfile != "") {  variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); }
 328         else { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); }
 329         string outputFileName = getOutputFileName("database", variables);
 330         outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
 331
 332         ofstream out;
 333         m->openOutputFile(outputFileName, out);
 334
 335         string header = "OTUNumber\tAbundance\t";
 336
 337
 338         if (listfile != "") {
 339             //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
 340             ListVector* list = getList();
 341
 342             if (otuLabels.size() != list->getNumBins()) {
 343                 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;  }
 344
 345             if (m->control_pressed) { delete list; return 0; }
 346
 347             GroupMap* groupmap = NULL;
 348             if (groupfile != "") {
 349                 groupmap = new GroupMap(groupfile);
 350                 groupmap->readMap();
 351             }
 352
 353             if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
 354
 355             if (groupfile != "") {
 356                 header = "OTUNumber\t";
 357                 for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
 358             }else if (countfile != "") {
 359                 if (ct.hasGroupInfo()) {
 360                     header = "OTUNumber\t";
 361                     for (int i = 0; i < ct.getNamesOfGroups().size(); i++) { header += (ct.getNamesOfGroups())[i] + '\t'; }
 362                 }
 363             }
 364             header += "repSeqName\trepSeq\tOTUConTaxonomy";
 365             out << header << endl;
 366
 367             for (int i = 0; i < list->getNumBins(); i++) {
 368
 369                 if (m->control_pressed) { break; }
 370
 371                 out << otuLabels[i] << '\t';
 372
 373                 vector<string> binNames;
 374                 string bin = list->get(i);
 375                 m->splitAtComma(bin, binNames);
 376
 377                 string seqRepName = "";
 378                 int numSeqsRep = 0;
 379
 380                 if (countfile == "") {
 381                     sort(binNames.begin(), binNames.end());
 382                     bin = "";
 383                     for (int j = 0; j < binNames.size()-1; j++) {
 384                         bin += binNames[j] + ',';
 385                     }
 386                     bin += binNames[binNames.size()-1];
 387                     map<string, string>::iterator it = repNames.find(bin);
 388
 389                     if (it == repNames.end()) {
 390                         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;
 391                     }else { seqRepName = it->second;  numSeqsRep = binNames.size(); }
 392
 393                     //sanity check
 394                     if (binNames.size() != classifyOtuSizes[i]) {
 395                         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;
 396                     }
 397                 }else {
 398                     //find rep sequence in bin
 399                     for (int j = 0; j < binNames.size(); j++) {
 400                         map<string, int>::iterator itNameMap = nameMap.find(binNames[j]); //if you are in the counttable you must be the rep. because get.oturep with a countfile only includes the rep sequences in the rep.count file.
 401                         if (itNameMap != nameMap.end()) {
 402                             seqRepName = itNameMap->first;
 403                             numSeqsRep = itNameMap->second;
 404                             j += binNames.size();
 405                         }
 406                     }
 407
 408                     if (seqRepName == "") {
 409                         m->mothurOut("[ERROR: OTU " + otuLabels[i] + " is not in the count file. Make sure you are using files for the same distance.\n"); m->control_pressed = true;   break;
 410                     }
 411
 412                     if (numSeqsRep != classifyOtuSizes[i]) {
 413                         m->mothurOut("[ERROR: OTU " + otuLabels[i] + " contains " + toString(numSeqsRep) + " 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;
 414                     }
 415                 }
 416
 417                 //output abundances
 418                 if (groupfile != "") {
 419                     string groupAbunds = "";
 420                     map<string, int> counts;
 421                     //initialize counts to 0
 422                     for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
 423
 424                     //find abundances by group
 425                     bool error = false;
 426                     for (int j = 0; j < binNames.size(); j++) {
 427                         string group = groupmap->getGroup(binNames[j]);
 428                         if (group == "not found") {
 429                             m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
 430                             error = true;
 431                         }else { counts[group]++; }
 432                     }
 433
 434                     //output counts
 435                     for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t';  }
 436
 437                     if (error) { m->control_pressed = true; }
 438                 }else if (countfile != "") {
 439                     if (ct.hasGroupInfo()) {
 440                         vector<int> groupCounts = ct.getGroupCounts(seqRepName);
 441                         for (int j = 0; j < groupCounts.size(); j++) { out << groupCounts[j] << '\t';  }
 442                     }else { out << numSeqsRep << '\t'; }
 443                 }else { out << numSeqsRep << '\t'; }
 444
 445                 //output repSeq
 446                 out << seqRepName << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
 447             }
 448
 449
 450             delete list;
 451             if (groupfile != "") { delete groupmap; }
 452
 453         }else {
 454             vector<SharedRAbundVector*> lookup = getShared();
 455
 456             header = "OTUNumber\t";
 457             for (int i = 0; i < lookup.size(); i++) { header += lookup[i]->getGroup() + '\t'; }
 458             header += "repSeqName\trepSeq\tOTUConTaxonomy";
 459             out << header << endl;
 460
 461             for (int h = 0; h < lookup[0]->getNumBins(); h++) {
 462
 463                 if (m->control_pressed) { break; }
 464
 465                 int index = findIndex(otuLabels, m->currentBinLabels[h]);
 466                 if (index == -1) {  m->mothurOut("[ERROR]: " + m->currentBinLabels[h] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
 467
 468                 if (m->control_pressed) { break; }
 469
 470                 out << otuLabels[index] << '\t';
 471
 472                 int totalAbund = 0;
 473                 for (int i = 0; i < lookup.size(); i++) {
 474                     int abund = lookup[i]->getAbundance(h);
 475                     totalAbund += abund;
 476                     out << abund << '\t';
 477                 }
 478
 479                 //sanity check
 480                 if (totalAbund != classifyOtuSizes[index]) {
 481                     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;
 482                 }
 483
 484                 //output repSeq
 485                 out << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
 486             }
 487         }
 488         out.close();
 489         if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 490
 491         m->mothurOutEndLine();
 492                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 493                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 494                 m->mothurOutEndLine();
 495
 496         return 0;
 497
 498     }
 499         catch(exception& e) {
 500                 m->errorOut(e, "CreateDatabaseCommand", "execute");
 501                 exit(1);
 502         }
 503 }
 504 //**********************************************************************************************************************
 505 int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
 506         try {
 507         int index = -1;
 508         for (int i = 0; i < otuLabels.size(); i++) {
 509             if (otuLabels[i] == label) { index = i; break; }
 510         }
 511                 return index;
 512     }
 513         catch(exception& e) {
 514                 m->errorOut(e, "CreateDatabaseCommand", "findIndex");
 515                 exit(1);
 516         }
 517 }
 518 //**********************************************************************************************************************
 519 vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<string>& otuLabels){
 520         try {
 521
 522         vector<int> sizes;
 523
 524         ifstream in;
 525         m->openInputFile(contaxonomyfile, in);
 526
 527         //read headers
 528         m->getline(in);
 529
 530         while (!in.eof()) {
 531
 532             if (m->control_pressed) { break; }
 533
 534             string otu = ""; string tax = "unknown";
 535             int size = 0;
 536
 537             in >> otu >> size >> tax; m->gobble(in);
 538
 539             sizes.push_back(size);
 540             taxonomies.push_back(tax);
 541             otuLabels.push_back(otu);
 542         }
 543         in.close();
 544
 545         return sizes;
 546     }
 547         catch(exception& e) {
 548                 m->errorOut(e, "CreateDatabaseCommand", "readTax");
 549                 exit(1);
 550         }
 551 }
 552 //**********************************************************************************************************************
 553 vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
 554         try {
 555
 556         vector<int> sizes;
 557
 558         ifstream in;
 559         m->openInputFile(repfastafile, in);
 560
 561         set<int> sanity;
 562         while (!in.eof()) {
 563
 564             if (m->control_pressed) { break; }
 565
 566             string binInfo;
 567             Sequence seq(in, binInfo, true);  m->gobble(in);
 568
 569             //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
 570             vector<string> info;
 571             m->splitAtChar(binInfo, info, '|');
 572             //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;}
 573
 574             int size = 0;
 575             m->mothurConvert(info[1], size);
 576
 577             int binNumber = 0;
 578             string temp = "";
 579             for (int i = 0; i < info[0].size(); i++) { if (isspace(info[0][i])) {;}else{temp +=info[0][i]; } }
 580             m->mothurConvert(temp, binNumber);
 581             set<int>::iterator it = sanity.find(binNumber);
 582             if (it != sanity.end()) {
 583                 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;
 584             }else { sanity.insert(binNumber); }
 585
 586             sizes.push_back(size);
 587             seqs.push_back(seq);
 588         }
 589         in.close();
 590
 591         return sizes;
 592     }
 593         catch(exception& e) {
 594                 m->errorOut(e, "CreateDatabaseCommand", "readFasta");
 595                 exit(1);
 596         }
 597 }
 598 //**********************************************************************************************************************
 599 ListVector* CreateDatabaseCommand::getList(){
 600         try {
 601                 InputData* input = new InputData(listfile, "list");
 602                 ListVector* list = input->getListVector();
 603                 string lastLabel = list->getLabel();
 604
 605                 if (label == "") { label = lastLabel; delete input; return list; }
 606
 607                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 608                 set<string> labels; labels.insert(label);
 609                 set<string> processedLabels;
 610                 set<string> userLabels = labels;
 611
 612                 //as long as you are not at the end of the file or done wih the lines you want
 613                 while((list != NULL) && (userLabels.size() != 0)) {
 614                         if (m->control_pressed) {  delete input; return list;  }
 615
 616                         if(labels.count(list->getLabel()) == 1){
 617                                 processedLabels.insert(list->getLabel());
 618                                 userLabels.erase(list->getLabel());
 619                                 break;
 620                         }
 621
 622                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 623                                 string saveLabel = list->getLabel();
 624
 625                                 delete list;
 626                                 list = input->getListVector(lastLabel);
 627
 628                                 processedLabels.insert(list->getLabel());
 629                                 userLabels.erase(list->getLabel());
 630
 631                                 //restore real lastlabel to save below
 632                                 list->setLabel(saveLabel);
 633                                 break;
 634                         }
 635
 636                         lastLabel = list->getLabel();
 637
 638                         //get next line to process
 639                         //prevent memory leak
 640                         delete list;
 641                         list = input->getListVector();
 642                 }
 643
 644
 645                 if (m->control_pressed) { delete input; return list;  }
 646
 647                 //output error messages about any remaining user labels
 648                 set<string>::iterator it;
 649                 bool needToRun = false;
 650                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 651                         m->mothurOut("Your file does not include the label " + *it);
 652                         if (processedLabels.count(lastLabel) != 1) {
 653                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 654                                 needToRun = true;
 655                         }else {
 656                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 657                         }
 658                 }
 659
 660                 //run last label if you need to
 661                 if (needToRun == true)  {
 662                         delete list;
 663                         list = input->getListVector(lastLabel);
 664                 }
 665
 666                 delete input;
 667
 668         return list;
 669     }
 670         catch(exception& e) {
 671                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 672                 exit(1);
 673         }
 674 }
 675 //**********************************************************************************************************************
 676 vector<SharedRAbundVector*> CreateDatabaseCommand::getShared(){
 677         try {
 678                 InputData input(sharedfile, "sharedfile");
 679                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 680                 string lastLabel = lookup[0]->getLabel();
 681
 682                 if (label == "") { label = lastLabel; return lookup; }
 683
 684                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 685                 set<string> labels; labels.insert(label);
 686                 set<string> processedLabels;
 687                 set<string> userLabels = labels;
 688
 689                 //as long as you are not at the end of the file or done wih the lines you want
 690                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 691                         if (m->control_pressed) {  return lookup;  }
 692
 693                         if(labels.count(lookup[0]->getLabel()) == 1){
 694                                 processedLabels.insert(lookup[0]->getLabel());
 695                                 userLabels.erase(lookup[0]->getLabel());
 696                                 break;
 697                         }
 698
 699                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 700                                 string saveLabel = lookup[0]->getLabel();
 701
 702                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 703                                 lookup = input.getSharedRAbundVectors(lastLabel);
 704
 705                                 processedLabels.insert(lookup[0]->getLabel());
 706                                 userLabels.erase(lookup[0]->getLabel());
 707
 708                                 //restore real lastlabel to save below
 709                                 lookup[0]->setLabel(saveLabel);
 710                                 break;
 711                         }
 712
 713                         lastLabel = lookup[0]->getLabel();
 714
 715                         //get next line to process
 716                         //prevent memory leak
 717                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 718                         lookup = input.getSharedRAbundVectors();
 719                 }
 720
 721
 722                 if (m->control_pressed) { return lookup;  }
 723
 724                 //output error messages about any remaining user labels
 725                 set<string>::iterator it;
 726                 bool needToRun = false;
 727                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 728                         m->mothurOut("Your file does not include the label " + *it);
 729                         if (processedLabels.count(lastLabel) != 1) {
 730                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 731                                 needToRun = true;
 732                         }else {
 733                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 734                         }
 735                 }
 736
 737                 //run last label if you need to
 738                 if (needToRun == true)  {
 739                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 740                         lookup = input.getSharedRAbundVectors(lastLabel);
 741                 }
 742
 743         return lookup;
 744     }
 745         catch(exception& e) {
 746                 m->errorOut(e, "CreateDatabaseCommand", "getShared");
 747                 exit(1);
 748         }
 749 }
 750
 751 //**********************************************************************************************************************
 752
 753