summarycommand.cpp

   1 /*
   2  *  summarycommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "summarycommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "simpsoneven.h"
  18 #include "invsimpson.h"
  19 #include "npshannon.h"
  20 #include "shannon.h"
  21 #include "heip.h"
  22 #include "smithwilson.h"
  23 #include "shannoneven.h"
  24 #include "jackknife.h"
  25 #include "geom.h"
  26 #include "logsd.h"
  27 #include "qstat.h"
  28 #include "bergerparker.h"
  29 #include "bstick.h"
  30 #include "goodscoverage.h"
  31 #include "coverage.h"
  32 #include "efron.h"
  33 #include "boneh.h"
  34 #include "solow.h"
  35 #include "shen.h"
  36
  37 //**********************************************************************************************************************
  38
  39 SummaryCommand::SummaryCommand(string option)  {
  40         try {
  41                 globaldata = GlobalData::getInstance();
  42                 abort = false;
  43                 allLines = 1;
  44                 labels.clear();
  45                 Estimators.clear();
  46
  47                 //allow user to run help
  48                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
  49
  50                 else {
  51                         //valid paramters for this command
  52                         string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
  53                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  54
  55                         OptionParser parser(option);
  56                         map<string,string> parameters = parser.getParameters();
  57
  58                         ValidParameters validParameter;
  59
  60                         //check to make sure all parameters are valid for command
  61                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  62                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  63                         }
  64
  65                         //make sure the user has already run the read.otu command
  66                         if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); m->mothurOutEndLine(); abort = true; }
  67
  68                         //if the user changes the output directory command factory will send this info to us in the output parameter
  69                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  70                                 outputDir = "";
  71                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  72                         }
  73
  74                         //check for optional parameter and set defaults
  75                         // ...at some point should added some additional type checking...
  76                         label = validParameter.validFile(parameters, "label", false);
  77                         if (label == "not found") { label = ""; }
  78                         else {
  79                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
  80                                 else { allLines = 1;  }
  81                         }
  82
  83                         //if the user has not specified any labels use the ones from read.otu
  84                         if(label == "") {
  85                                 allLines = globaldata->allLines;
  86                                 labels = globaldata->labels;
  87                         }
  88
  89                         calc = validParameter.validFile(parameters, "calc", false);
  90                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
  91                         else {
  92                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
  93                         }
  94                         m->splitAtDash(calc, Estimators);
  95
  96                         string temp;
  97                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
  98                         convert(temp, abund);
  99
 100                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 101                         convert(temp, size);
 102
 103                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "F"; }
 104                         groupMode = m->isTrue(temp);
 105
 106
 107                 }
 108         }
 109         catch(exception& e) {
 110                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 111                 exit(1);
 112         }
 113 }
 114 //**********************************************************************************************************************
 115
 116 void SummaryCommand::help(){
 117         try {
 118                 m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 119                 m->mothurOut("The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
 120                 m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode.  No parameters are required.\n");
 121                 m->mothurOut("The summary.single command should be in the following format: \n");
 122                 m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
 123                 m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
 124                 validCalculator->printCalc("summary", cout);
 125                 m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
 126                 m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=False).\n");
 127                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 128                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 129         }
 130         catch(exception& e) {
 131                 m->errorOut(e, "SummaryCommand", "help");
 132                 exit(1);
 133         }
 134 }
 135
 136 //**********************************************************************************************************************
 137
 138 SummaryCommand::~SummaryCommand(){}
 139
 140 //**********************************************************************************************************************
 141
 142 int SummaryCommand::execute(){
 143         try {
 144
 145                 if (abort == true) { return 0; }
 146
 147                 vector<string> outputNames;
 148
 149                 string hadShared = "";
 150                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 151                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 152
 153                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 154
 155                 int numLines = 0;
 156                 int numCols = 0;
 157
 158                 for (int p = 0; p < inputFileNames.size(); p++) {
 159
 160                         numLines = 0;
 161                         numCols = 0;
 162
 163                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 164                         globaldata->inputFileName = inputFileNames[p];
 165                         outputNames.push_back(fileNameRoot);
 166
 167                         if (inputFileNames.size() > 1) {
 168                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 169                         }
 170
 171                         sumCalculators.clear();
 172
 173                         validCalculator = new ValidCalculators();
 174
 175                         for (int i=0; i<Estimators.size(); i++) {
 176                                 if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
 177                                         if(Estimators[i] == "sobs"){
 178                                                 sumCalculators.push_back(new Sobs());
 179                                         }else if(Estimators[i] == "chao"){
 180                                                 sumCalculators.push_back(new Chao1());
 181                                         }else if(Estimators[i] == "coverage"){
 182                                                 sumCalculators.push_back(new Coverage());
 183                                         }else if(Estimators[i] == "geometric"){
 184                                                 sumCalculators.push_back(new Geom());
 185                                         }else if(Estimators[i] == "logseries"){
 186                                                 sumCalculators.push_back(new LogSD());
 187                                         }else if(Estimators[i] == "qstat"){
 188                                                 sumCalculators.push_back(new QStat());
 189                                         }else if(Estimators[i] == "bergerparker"){
 190                                                 sumCalculators.push_back(new BergerParker());
 191                                         }else if(Estimators[i] == "bstick"){
 192                                                 sumCalculators.push_back(new BStick());
 193                                         }else if(Estimators[i] == "ace"){
 194                                                 if(abund < 5)
 195                                                         abund = 10;
 196                                                 sumCalculators.push_back(new Ace(abund));
 197                                         }else if(Estimators[i] == "jack"){
 198                                                 sumCalculators.push_back(new Jackknife());
 199                                         }else if(Estimators[i] == "shannon"){
 200                                                 sumCalculators.push_back(new Shannon());
 201                                         }else if(Estimators[i] == "shannoneven"){
 202                                                 sumCalculators.push_back(new ShannonEven());
 203                                         }else if(Estimators[i] == "npshannon"){
 204                                                 sumCalculators.push_back(new NPShannon());
 205                                         }else if(Estimators[i] == "heip"){
 206                                                 sumCalculators.push_back(new Heip());
 207                                         }else if(Estimators[i] == "smithwilson"){
 208                                                 sumCalculators.push_back(new SmithWilson());
 209                                         }else if(Estimators[i] == "simpson"){
 210                                                 sumCalculators.push_back(new Simpson());
 211                                         }else if(Estimators[i] == "simpsoneven"){
 212                                                 sumCalculators.push_back(new SimpsonEven());
 213                                         }else if(Estimators[i] == "invsimpson"){
 214                                                 sumCalculators.push_back(new InvSimpson());
 215                                         }else if(Estimators[i] == "bootstrap"){
 216                                                 sumCalculators.push_back(new Bootstrap());
 217                                         }else if (Estimators[i] == "nseqs") {
 218                                                 sumCalculators.push_back(new NSeqs());
 219                                         }else if (Estimators[i] == "goodscoverage") {
 220                                                 sumCalculators.push_back(new GoodsCoverage());
 221                                         }else if (Estimators[i] == "efron") {
 222                                                 sumCalculators.push_back(new Efron(size));
 223                                         }else if (Estimators[i] == "boneh") {
 224                                                 sumCalculators.push_back(new Boneh(size));
 225                                         }else if (Estimators[i] == "solow") {
 226                                                 sumCalculators.push_back(new Solow(size));
 227                                         }else if (Estimators[i] == "shen") {
 228                                                 sumCalculators.push_back(new Shen(size, abund));
 229                                         }
 230                                 }
 231                         }
 232
 233                         //if the users entered no valid calculators don't execute command
 234                         if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 235
 236                         ofstream outputFileHandle;
 237                         m->openOutputFile(fileNameRoot, outputFileHandle);
 238                         outputFileHandle << "label";
 239
 240                         read = new ReadOTUFile(globaldata->inputFileName);
 241                         read->read(&*globaldata);
 242
 243                         sabund = globaldata->sabund;
 244                         string lastLabel = sabund->getLabel();
 245                         input = globaldata->ginput;
 246
 247                         for(int i=0;i<sumCalculators.size();i++){
 248                                 if(sumCalculators[i]->getCols() == 1){
 249                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 250                                         numCols++;
 251                                 }
 252                                 else{
 253                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 254                                         numCols += 3;
 255                                 }
 256                         }
 257                         outputFileHandle << endl;
 258
 259                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 260                         set<string> processedLabels;
 261                         set<string> userLabels = labels;
 262
 263                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 264
 265                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 266
 267                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 268
 269                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 270
 271                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 272                                         processedLabels.insert(sabund->getLabel());
 273                                         userLabels.erase(sabund->getLabel());
 274
 275                                         outputFileHandle << sabund->getLabel();
 276                                         for(int i=0;i<sumCalculators.size();i++){
 277                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 278
 279                                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 280
 281                                                 outputFileHandle << '\t';
 282                                                 sumCalculators[i]->print(outputFileHandle);
 283                                         }
 284                                         outputFileHandle << endl;
 285                                         numLines++;
 286                                 }
 287
 288                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 289                                         string saveLabel = sabund->getLabel();
 290
 291                                         delete sabund;
 292                                         sabund = input->getSAbundVector(lastLabel);
 293
 294                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 295                                         processedLabels.insert(sabund->getLabel());
 296                                         userLabels.erase(sabund->getLabel());
 297
 298                                         outputFileHandle << sabund->getLabel();
 299                                         for(int i=0;i<sumCalculators.size();i++){
 300                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 301
 302                                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 303
 304                                                 outputFileHandle << '\t';
 305                                                 sumCalculators[i]->print(outputFileHandle);
 306                                         }
 307                                         outputFileHandle << endl;
 308                                         numLines++;
 309
 310                                         //restore real lastlabel to save below
 311                                         sabund->setLabel(saveLabel);
 312                                 }
 313
 314                                 lastLabel = sabund->getLabel();
 315
 316                                 delete sabund;
 317                                 sabund = input->getSAbundVector();
 318                         }
 319
 320                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 321
 322                         //output error messages about any remaining user labels
 323                         set<string>::iterator it;
 324                         bool needToRun = false;
 325                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 326                                 m->mothurOut("Your file does not include the label " + *it);
 327                                 if (processedLabels.count(lastLabel) != 1) {
 328                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 329                                         needToRun = true;
 330                                 }else {
 331                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 332                                 }
 333                         }
 334
 335                         //run last label if you need to
 336                         if (needToRun == true)  {
 337                                 if (sabund != NULL) {   delete sabund;  }
 338                                 sabund = input->getSAbundVector(lastLabel);
 339
 340                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 341                                 outputFileHandle << sabund->getLabel();
 342                                 for(int i=0;i<sumCalculators.size();i++){
 343                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 344
 345                                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 346
 347                                         outputFileHandle << '\t';
 348                                         sumCalculators[i]->print(outputFileHandle);
 349                                 }
 350                                 outputFileHandle << endl;
 351                                 numLines++;
 352                                 delete sabund;
 353                         }
 354
 355                         outputFileHandle.close();
 356
 357                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 358
 359
 360                         delete input;  globaldata->ginput = NULL;
 361                         delete read;
 362                         delete validCalculator;
 363                         globaldata->sabund = NULL;
 364                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 365                 }
 366
 367                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 368
 369                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 370
 371                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 372                 if ((hadShared != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 373
 374                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 375
 376                 m->mothurOutEndLine();
 377                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 378                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 379                 m->mothurOutEndLine();
 380
 381                 return 0;
 382         }
 383         catch(exception& e) {
 384                 m->errorOut(e, "SummaryCommand", "execute");
 385                 exit(1);
 386         }
 387 }
 388 //**********************************************************************************************************************
 389 vector<string> SummaryCommand::parseSharedFile(string filename) {
 390         try {
 391                 vector<string> filenames;
 392
 393                 map<string, ofstream*> filehandles;
 394                 map<string, ofstream*>::iterator it3;
 395
 396
 397                 //read first line
 398                 read = new ReadOTUFile(filename);
 399                 read->read(&*globaldata);
 400
 401                 input = globaldata->ginput;
 402                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 403
 404                 string sharedFileRoot = m->getRootName(filename);
 405
 406                 //clears file before we start to write to it below
 407                 for (int i=0; i<lookup.size(); i++) {
 408                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 409                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 410                 }
 411
 412                 ofstream* temp;
 413                 for (int i=0; i<lookup.size(); i++) {
 414                         temp = new ofstream;
 415                         filehandles[lookup[i]->getGroup()] = temp;
 416                         groups.push_back(lookup[i]->getGroup());
 417                 }
 418
 419                 while(lookup[0] != NULL) {
 420
 421                         for (int i = 0; i < lookup.size(); i++) {
 422                                 RAbundVector rav = lookup[i]->getRAbundVector();
 423                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 424                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 425                                 (*(filehandles[lookup[i]->getGroup()])).close();
 426                         }
 427
 428                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 429                         lookup = input->getSharedRAbundVectors();
 430                 }
 431
 432                 //free memory
 433                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 434                         delete it3->second;
 435                 }
 436                 delete read;
 437                 delete input;
 438                 globaldata->ginput = NULL;
 439
 440                 return filenames;
 441         }
 442         catch(exception& e) {
 443                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 444                 exit(1);
 445         }
 446 }
 447 //**********************************************************************************************************************
 448 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string> outputNames) {
 449         try {
 450
 451                 ofstream out;
 452                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
 453
 454                 //open combined file
 455                 m->openOutputFile(combineFileName, out);
 456
 457                 //open each groups summary file
 458                 string newLabel = "";
 459                 ifstream* temp;
 460                 map<string, ifstream*> filehandles;
 461                 for (int i=0; i<outputNames.size(); i++) {
 462                         temp = new ifstream;
 463                         filehandles[outputNames[i]] = temp;
 464                         m->openInputFile(outputNames[i], *(temp));
 465
 466                         //read through first line - labels
 467                         string tempLabel;
 468                         if (i == 0) { //we want to save the labels to output below
 469                                 for (int j = 0; j < numCols+1; j++) {
 470                                         *(temp) >> tempLabel;
 471
 472                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 473                                         }else{  newLabel += tempLabel + '\t';   }
 474                                 }
 475                         }else{  for (int j = 0; j < numCols+1; j++) {  *(temp) >> tempLabel;  }  }
 476
 477                         m->gobble(*(temp));
 478                 }
 479
 480                 //output label line to new file
 481                 out << newLabel << endl;
 482
 483                 //for each label
 484                 for (int i = 0; i < numLines; i++) {
 485
 486                         //grab summary data for each group
 487                         for (int i=0; i<outputNames.size(); i++) {
 488                                 string tempLabel;
 489
 490                                 for (int j = 0; j < numCols+1; j++) {
 491                                         *(filehandles[outputNames[i]]) >> tempLabel;
 492
 493                                         //print to combined file
 494                                         if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t';    }
 495                                         else{  out << tempLabel << '\t';        }
 496                                 }
 497
 498                                 out << endl;
 499                                 m->gobble(*(filehandles[outputNames[i]]));
 500                         }
 501                 }
 502
 503                 //close each groups summary file
 504                 for (int i=0; i<outputNames.size(); i++) {  (*(filehandles[outputNames[i]])).close();  }
 505                 out.close();
 506
 507                 //return combine file name
 508                 return combineFileName;
 509
 510         }
 511         catch(exception& e) {
 512                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 513                 exit(1);
 514         }
 515 }
 516 //**********************************************************************************************************************