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 vector<string> SummaryCommand::getValidParameters(){
  39         try {
  40                 string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "SummaryCommand", "getValidParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 SummaryCommand::SummaryCommand(){
  51         try {
  52                 abort = true;
  53                 //initialize outputTypes
  54                 vector<string> tempOutNames;
  55                 outputTypes["summary"] = tempOutNames;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 vector<string> SummaryCommand::getRequiredParameters(){
  64         try {
  65                 vector<string> myArray;
  66                 return myArray;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "SummaryCommand", "getRequiredParameters");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 vector<string> SummaryCommand::getRequiredFiles(){
  75         try {
  76                 string AlignArray[] =  {"shared","list","rabund","sabund","or"};
  77                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  78                 return myArray;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "SummaryCommand", "getRequiredFiles");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86
  87 SummaryCommand::SummaryCommand(string option)  {
  88         try {
  89                 globaldata = GlobalData::getInstance();
  90                 abort = false;
  91                 allLines = 1;
  92                 labels.clear();
  93                 Estimators.clear();
  94
  95                 //allow user to run help
  96                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
  97
  98                 else {
  99                         //valid paramters for this command
 100                         string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
 101                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 102
 103                         OptionParser parser(option);
 104                         map<string,string> parameters = parser.getParameters();
 105
 106                         ValidParameters validParameter;
 107
 108                         //check to make sure all parameters are valid for command
 109                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 110                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 111                         }
 112
 113                         //initialize outputTypes
 114                         vector<string> tempOutNames;
 115                         outputTypes["summary"] = tempOutNames;
 116
 117                         //make sure the user has already run the read.otu command
 118                         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; }
 119
 120                         //if the user changes the output directory command factory will send this info to us in the output parameter
 121                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 122                                 outputDir = "";
 123                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 124                         }
 125
 126                         //check for optional parameter and set defaults
 127                         // ...at some point should added some additional type checking...
 128                         label = validParameter.validFile(parameters, "label", false);
 129                         if (label == "not found") { label = ""; }
 130                         else {
 131                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 132                                 else { allLines = 1;  }
 133                         }
 134
 135                         //if the user has not specified any labels use the ones from read.otu
 136                         if(label == "") {
 137                                 allLines = globaldata->allLines;
 138                                 labels = globaldata->labels;
 139                         }
 140
 141                         calc = validParameter.validFile(parameters, "calc", false);
 142                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 143                         else {
 144                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 145                         }
 146                         m->splitAtDash(calc, Estimators);
 147
 148                         string temp;
 149                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 150                         convert(temp, abund);
 151
 152                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 153                         convert(temp, size);
 154
 155                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 156                         groupMode = m->isTrue(temp);
 157
 158
 159                 }
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 163                 exit(1);
 164         }
 165 }
 166 //**********************************************************************************************************************
 167
 168 void SummaryCommand::help(){
 169         try {
 170                 m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 171                 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");
 172                 m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode.  No parameters are required.\n");
 173                 m->mothurOut("The summary.single command should be in the following format: \n");
 174                 m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
 175                 m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
 176                 validCalculator->printCalc("summary", cout);
 177                 m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
 178                 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=true).\n");
 179                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 180                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "SummaryCommand", "help");
 184                 exit(1);
 185         }
 186 }
 187
 188 //**********************************************************************************************************************
 189
 190 SummaryCommand::~SummaryCommand(){}
 191
 192 //**********************************************************************************************************************
 193
 194 int SummaryCommand::execute(){
 195         try {
 196
 197                 if (abort == true) { return 0; }
 198
 199                 string hadShared = "";
 200                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 201                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 202
 203                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 204
 205                 int numLines = 0;
 206                 int numCols = 0;
 207
 208                 for (int p = 0; p < inputFileNames.size(); p++) {
 209
 210                         numLines = 0;
 211                         numCols = 0;
 212
 213                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 214                         globaldata->inputFileName = inputFileNames[p];
 215                         outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
 216
 217                         if (inputFileNames.size() > 1) {
 218                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 219                         }
 220
 221                         sumCalculators.clear();
 222
 223                         validCalculator = new ValidCalculators();
 224
 225                         for (int i=0; i<Estimators.size(); i++) {
 226                                 if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
 227                                         if(Estimators[i] == "sobs"){
 228                                                 sumCalculators.push_back(new Sobs());
 229                                         }else if(Estimators[i] == "chao"){
 230                                                 sumCalculators.push_back(new Chao1());
 231                                         }else if(Estimators[i] == "coverage"){
 232                                                 sumCalculators.push_back(new Coverage());
 233                                         }else if(Estimators[i] == "geometric"){
 234                                                 sumCalculators.push_back(new Geom());
 235                                         }else if(Estimators[i] == "logseries"){
 236                                                 sumCalculators.push_back(new LogSD());
 237                                         }else if(Estimators[i] == "qstat"){
 238                                                 sumCalculators.push_back(new QStat());
 239                                         }else if(Estimators[i] == "bergerparker"){
 240                                                 sumCalculators.push_back(new BergerParker());
 241                                         }else if(Estimators[i] == "bstick"){
 242                                                 sumCalculators.push_back(new BStick());
 243                                         }else if(Estimators[i] == "ace"){
 244                                                 if(abund < 5)
 245                                                         abund = 10;
 246                                                 sumCalculators.push_back(new Ace(abund));
 247                                         }else if(Estimators[i] == "jack"){
 248                                                 sumCalculators.push_back(new Jackknife());
 249                                         }else if(Estimators[i] == "shannon"){
 250                                                 sumCalculators.push_back(new Shannon());
 251                                         }else if(Estimators[i] == "shannoneven"){
 252                                                 sumCalculators.push_back(new ShannonEven());
 253                                         }else if(Estimators[i] == "npshannon"){
 254                                                 sumCalculators.push_back(new NPShannon());
 255                                         }else if(Estimators[i] == "heip"){
 256                                                 sumCalculators.push_back(new Heip());
 257                                         }else if(Estimators[i] == "smithwilson"){
 258                                                 sumCalculators.push_back(new SmithWilson());
 259                                         }else if(Estimators[i] == "simpson"){
 260                                                 sumCalculators.push_back(new Simpson());
 261                                         }else if(Estimators[i] == "simpsoneven"){
 262                                                 sumCalculators.push_back(new SimpsonEven());
 263                                         }else if(Estimators[i] == "invsimpson"){
 264                                                 sumCalculators.push_back(new InvSimpson());
 265                                         }else if(Estimators[i] == "bootstrap"){
 266                                                 sumCalculators.push_back(new Bootstrap());
 267                                         }else if (Estimators[i] == "nseqs") {
 268                                                 sumCalculators.push_back(new NSeqs());
 269                                         }else if (Estimators[i] == "goodscoverage") {
 270                                                 sumCalculators.push_back(new GoodsCoverage());
 271                                         }else if (Estimators[i] == "efron") {
 272                                                 sumCalculators.push_back(new Efron(size));
 273                                         }else if (Estimators[i] == "boneh") {
 274                                                 sumCalculators.push_back(new Boneh(size));
 275                                         }else if (Estimators[i] == "solow") {
 276                                                 sumCalculators.push_back(new Solow(size));
 277                                         }else if (Estimators[i] == "shen") {
 278                                                 sumCalculators.push_back(new Shen(size, abund));
 279                                         }
 280                                 }
 281                         }
 282
 283                         //if the users entered no valid calculators don't execute command
 284                         if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 285
 286                         ofstream outputFileHandle;
 287                         m->openOutputFile(fileNameRoot, outputFileHandle);
 288                         outputFileHandle << "label";
 289
 290                         read = new ReadOTUFile(globaldata->inputFileName);
 291                         read->read(&*globaldata);
 292
 293                         sabund = globaldata->sabund;
 294                         string lastLabel = sabund->getLabel();
 295                         input = globaldata->ginput;
 296
 297                         for(int i=0;i<sumCalculators.size();i++){
 298                                 if(sumCalculators[i]->getCols() == 1){
 299                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 300                                         numCols++;
 301                                 }
 302                                 else{
 303                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 304                                         numCols += 3;
 305                                 }
 306                         }
 307                         outputFileHandle << endl;
 308
 309                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 310                         set<string> processedLabels;
 311                         set<string> userLabels = labels;
 312
 313                         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;  }
 314
 315                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 316
 317                                 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;  }
 318
 319                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 320
 321                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 322                                         processedLabels.insert(sabund->getLabel());
 323                                         userLabels.erase(sabund->getLabel());
 324
 325                                         outputFileHandle << sabund->getLabel();
 326                                         for(int i=0;i<sumCalculators.size();i++){
 327                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 328
 329                                                 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;  }
 330
 331                                                 outputFileHandle << '\t';
 332                                                 sumCalculators[i]->print(outputFileHandle);
 333                                         }
 334                                         outputFileHandle << endl;
 335                                         numLines++;
 336                                 }
 337
 338                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 339                                         string saveLabel = sabund->getLabel();
 340
 341                                         delete sabund;
 342                                         sabund = input->getSAbundVector(lastLabel);
 343
 344                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 345                                         processedLabels.insert(sabund->getLabel());
 346                                         userLabels.erase(sabund->getLabel());
 347
 348                                         outputFileHandle << sabund->getLabel();
 349                                         for(int i=0;i<sumCalculators.size();i++){
 350                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 351
 352                                                 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;  }
 353
 354                                                 outputFileHandle << '\t';
 355                                                 sumCalculators[i]->print(outputFileHandle);
 356                                         }
 357                                         outputFileHandle << endl;
 358                                         numLines++;
 359
 360                                         //restore real lastlabel to save below
 361                                         sabund->setLabel(saveLabel);
 362                                 }
 363
 364                                 lastLabel = sabund->getLabel();
 365
 366                                 delete sabund;
 367                                 sabund = input->getSAbundVector();
 368                         }
 369
 370                         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;  }
 371
 372                         //output error messages about any remaining user labels
 373                         set<string>::iterator it;
 374                         bool needToRun = false;
 375                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 376                                 m->mothurOut("Your file does not include the label " + *it);
 377                                 if (processedLabels.count(lastLabel) != 1) {
 378                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 379                                         needToRun = true;
 380                                 }else {
 381                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 382                                 }
 383                         }
 384
 385                         //run last label if you need to
 386                         if (needToRun == true)  {
 387                                 if (sabund != NULL) {   delete sabund;  }
 388                                 sabund = input->getSAbundVector(lastLabel);
 389
 390                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 391                                 outputFileHandle << sabund->getLabel();
 392                                 for(int i=0;i<sumCalculators.size();i++){
 393                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 394
 395                                         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;  }
 396
 397                                         outputFileHandle << '\t';
 398                                         sumCalculators[i]->print(outputFileHandle);
 399                                 }
 400                                 outputFileHandle << endl;
 401                                 numLines++;
 402                                 delete sabund;
 403                         }
 404
 405                         outputFileHandle.close();
 406
 407                         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;  }
 408
 409
 410                         delete input;  globaldata->ginput = NULL;
 411                         delete read;
 412                         delete validCalculator;
 413                         globaldata->sabund = NULL;
 414                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 415                 }
 416
 417                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 418
 419                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 420
 421                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 422                 if ((hadShared != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 423
 424                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 425
 426                 m->mothurOutEndLine();
 427                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 428                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 429                 m->mothurOutEndLine();
 430
 431                 return 0;
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "SummaryCommand", "execute");
 435                 exit(1);
 436         }
 437 }
 438 //**********************************************************************************************************************
 439 vector<string> SummaryCommand::parseSharedFile(string filename) {
 440         try {
 441                 vector<string> filenames;
 442
 443                 map<string, ofstream*> filehandles;
 444                 map<string, ofstream*>::iterator it3;
 445
 446
 447                 //read first line
 448                 read = new ReadOTUFile(filename);
 449                 read->read(&*globaldata);
 450
 451                 input = globaldata->ginput;
 452                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 453
 454                 string sharedFileRoot = m->getRootName(filename);
 455
 456                 //clears file before we start to write to it below
 457                 for (int i=0; i<lookup.size(); i++) {
 458                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 459                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 460                 }
 461
 462                 ofstream* temp;
 463                 for (int i=0; i<lookup.size(); i++) {
 464                         temp = new ofstream;
 465                         filehandles[lookup[i]->getGroup()] = temp;
 466                         groups.push_back(lookup[i]->getGroup());
 467                 }
 468
 469                 while(lookup[0] != NULL) {
 470
 471                         for (int i = 0; i < lookup.size(); i++) {
 472                                 RAbundVector rav = lookup[i]->getRAbundVector();
 473                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 474                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 475                                 (*(filehandles[lookup[i]->getGroup()])).close();
 476                         }
 477
 478                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 479                         lookup = input->getSharedRAbundVectors();
 480                 }
 481
 482                 //free memory
 483                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 484                         delete it3->second;
 485                 }
 486                 delete read;
 487                 delete input;
 488                 globaldata->ginput = NULL;
 489
 490                 return filenames;
 491         }
 492         catch(exception& e) {
 493                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 494                 exit(1);
 495         }
 496 }
 497 //**********************************************************************************************************************
 498 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
 499         try {
 500
 501                 ofstream out;
 502                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
 503
 504                 //open combined file
 505                 m->openOutputFile(combineFileName, out);
 506
 507                 //open each groups summary file
 508                 string newLabel = "";
 509                 map<string, vector<string> > files;
 510                 for (int i=0; i<outputNames.size(); i++) {
 511                         vector<string> thisFilesLines;
 512
 513                         ifstream temp;
 514                         m->openInputFile(outputNames[i], temp);
 515
 516                         //read through first line - labels
 517                         string tempLabel;
 518                         if (i == 0) { //we want to save the labels to output below
 519                                 for (int j = 0; j < numCols+1; j++) {
 520                                         temp >> tempLabel;
 521
 522                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 523                                         }else{  newLabel += tempLabel + '\t';   }
 524                                 }
 525                         }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
 526
 527                         m->gobble(temp);
 528
 529                         //for each label
 530                         for (int k = 0; k < numLines; k++) {
 531
 532                                 string thisLine = "";
 533                                 string tempLabel;
 534
 535                                 for (int j = 0; j < numCols+1; j++) {
 536                                         temp >> tempLabel;
 537
 538                                         //save for later
 539                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 540                                         else{  thisLine += tempLabel + "\t";    }
 541                                 }
 542
 543                                 thisLine += "\n";
 544
 545                                 thisFilesLines.push_back(thisLine);
 546
 547                                 m->gobble(temp);
 548                         }
 549
 550                         files[outputNames[i]] = thisFilesLines;
 551
 552                         temp.close();
 553                         remove(outputNames[i].c_str());
 554                 }
 555
 556                 //output label line to new file
 557                 out << newLabel << endl;
 558
 559                 //for each label
 560                 for (int k = 0; k < numLines; k++) {
 561
 562                         //grab summary data for each group
 563                         for (int i=0; i<outputNames.size(); i++) {
 564                                 out << files[outputNames[i]][k];
 565                         }
 566                 }
 567
 568                 outputNames.clear();
 569
 570                 out.close();
 571
 572                 //return combine file name
 573                 return combineFileName;
 574
 575         }
 576         catch(exception& e) {
 577                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 578                 exit(1);
 579         }
 580 }
 581 //**********************************************************************************************************************