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; calledHelp = true;
  53                 vector<string> tempOutNames;
  54                 outputTypes["summary"] = tempOutNames;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 vector<string> SummaryCommand::getRequiredParameters(){
  63         try {
  64                 vector<string> myArray;
  65                 return myArray;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "SummaryCommand", "getRequiredParameters");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 vector<string> SummaryCommand::getRequiredFiles(){
  74         try {
  75                 string AlignArray[] =  {"shared","list","rabund","sabund","or"};
  76                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  77                 return myArray;
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "SummaryCommand", "getRequiredFiles");
  81                 exit(1);
  82         }
  83 }
  84 //**********************************************************************************************************************
  85
  86 SummaryCommand::SummaryCommand(string option)  {
  87         try {
  88                 globaldata = GlobalData::getInstance();
  89                 abort = false; calledHelp = false;
  90                 allLines = 1;
  91                 labels.clear();
  92                 Estimators.clear();
  93
  94                 //allow user to run help
  95                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; calledHelp = true; }
  96
  97                 else {
  98                         //valid paramters for this command
  99                         string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
 100                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 101
 102                         OptionParser parser(option);
 103                         map<string,string> parameters = parser.getParameters();
 104
 105                         ValidParameters validParameter;
 106
 107                         //check to make sure all parameters are valid for command
 108                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 109                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 110                         }
 111
 112                         //initialize outputTypes
 113                         vector<string> tempOutNames;
 114                         outputTypes["summary"] = tempOutNames;
 115
 116                         //make sure the user has already run the read.otu command
 117                         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; }
 118
 119                         //if the user changes the output directory command factory will send this info to us in the output parameter
 120                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 121                                 outputDir = "";
 122                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 123                         }
 124
 125                         //check for optional parameter and set defaults
 126                         // ...at some point should added some additional type checking...
 127                         label = validParameter.validFile(parameters, "label", false);
 128                         if (label == "not found") { label = ""; }
 129                         else {
 130                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 131                                 else { allLines = 1;  }
 132                         }
 133
 134                         //if the user has not specified any labels use the ones from read.otu
 135                         if(label == "") {
 136                                 allLines = globaldata->allLines;
 137                                 labels = globaldata->labels;
 138                         }
 139
 140                         calc = validParameter.validFile(parameters, "calc", false);
 141                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 142                         else {
 143                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 144                         }
 145                         m->splitAtDash(calc, Estimators);
 146
 147                         string temp;
 148                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 149                         convert(temp, abund);
 150
 151                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 152                         convert(temp, size);
 153
 154                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 155                         groupMode = m->isTrue(temp);
 156
 157
 158                 }
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 162                 exit(1);
 163         }
 164 }
 165 //**********************************************************************************************************************
 166
 167 void SummaryCommand::help(){
 168         try {
 169                 m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 170                 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");
 171                 m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode.  No parameters are required.\n");
 172                 m->mothurOut("The summary.single command should be in the following format: \n");
 173                 m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
 174                 m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
 175                 validCalculator->printCalc("summary", cout);
 176                 m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
 177                 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");
 178                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 179                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 180         }
 181         catch(exception& e) {
 182                 m->errorOut(e, "SummaryCommand", "help");
 183                 exit(1);
 184         }
 185 }
 186
 187 //**********************************************************************************************************************
 188
 189 SummaryCommand::~SummaryCommand(){}
 190
 191 //**********************************************************************************************************************
 192
 193 int SummaryCommand::execute(){
 194         try {
 195
 196                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 197
 198                 string hadShared = "";
 199                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 200                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 201
 202                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 203
 204                 int numLines = 0;
 205                 int numCols = 0;
 206
 207                 for (int p = 0; p < inputFileNames.size(); p++) {
 208
 209                         numLines = 0;
 210                         numCols = 0;
 211
 212                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 213                         globaldata->inputFileName = inputFileNames[p];
 214                         outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
 215
 216                         if (inputFileNames.size() > 1) {
 217                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 218                         }
 219
 220                         sumCalculators.clear();
 221
 222                         validCalculator = new ValidCalculators();
 223
 224                         for (int i=0; i<Estimators.size(); i++) {
 225                                 if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
 226                                         if(Estimators[i] == "sobs"){
 227                                                 sumCalculators.push_back(new Sobs());
 228                                         }else if(Estimators[i] == "chao"){
 229                                                 sumCalculators.push_back(new Chao1());
 230                                         }else if(Estimators[i] == "coverage"){
 231                                                 sumCalculators.push_back(new Coverage());
 232                                         }else if(Estimators[i] == "geometric"){
 233                                                 sumCalculators.push_back(new Geom());
 234                                         }else if(Estimators[i] == "logseries"){
 235                                                 sumCalculators.push_back(new LogSD());
 236                                         }else if(Estimators[i] == "qstat"){
 237                                                 sumCalculators.push_back(new QStat());
 238                                         }else if(Estimators[i] == "bergerparker"){
 239                                                 sumCalculators.push_back(new BergerParker());
 240                                         }else if(Estimators[i] == "bstick"){
 241                                                 sumCalculators.push_back(new BStick());
 242                                         }else if(Estimators[i] == "ace"){
 243                                                 if(abund < 5)
 244                                                         abund = 10;
 245                                                 sumCalculators.push_back(new Ace(abund));
 246                                         }else if(Estimators[i] == "jack"){
 247                                                 sumCalculators.push_back(new Jackknife());
 248                                         }else if(Estimators[i] == "shannon"){
 249                                                 sumCalculators.push_back(new Shannon());
 250                                         }else if(Estimators[i] == "shannoneven"){
 251                                                 sumCalculators.push_back(new ShannonEven());
 252                                         }else if(Estimators[i] == "npshannon"){
 253                                                 sumCalculators.push_back(new NPShannon());
 254                                         }else if(Estimators[i] == "heip"){
 255                                                 sumCalculators.push_back(new Heip());
 256                                         }else if(Estimators[i] == "smithwilson"){
 257                                                 sumCalculators.push_back(new SmithWilson());
 258                                         }else if(Estimators[i] == "simpson"){
 259                                                 sumCalculators.push_back(new Simpson());
 260                                         }else if(Estimators[i] == "simpsoneven"){
 261                                                 sumCalculators.push_back(new SimpsonEven());
 262                                         }else if(Estimators[i] == "invsimpson"){
 263                                                 sumCalculators.push_back(new InvSimpson());
 264                                         }else if(Estimators[i] == "bootstrap"){
 265                                                 sumCalculators.push_back(new Bootstrap());
 266                                         }else if (Estimators[i] == "nseqs") {
 267                                                 sumCalculators.push_back(new NSeqs());
 268                                         }else if (Estimators[i] == "goodscoverage") {
 269                                                 sumCalculators.push_back(new GoodsCoverage());
 270                                         }else if (Estimators[i] == "efron") {
 271                                                 sumCalculators.push_back(new Efron(size));
 272                                         }else if (Estimators[i] == "boneh") {
 273                                                 sumCalculators.push_back(new Boneh(size));
 274                                         }else if (Estimators[i] == "solow") {
 275                                                 sumCalculators.push_back(new Solow(size));
 276                                         }else if (Estimators[i] == "shen") {
 277                                                 sumCalculators.push_back(new Shen(size, abund));
 278                                         }
 279                                 }
 280                         }
 281
 282                         //if the users entered no valid calculators don't execute command
 283                         if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 284
 285                         ofstream outputFileHandle;
 286                         m->openOutputFile(fileNameRoot, outputFileHandle);
 287                         outputFileHandle << "label";
 288
 289                         read = new ReadOTUFile(globaldata->inputFileName);
 290                         read->read(&*globaldata);
 291
 292                         sabund = globaldata->sabund;
 293                         string lastLabel = sabund->getLabel();
 294                         input = globaldata->ginput;
 295
 296                         for(int i=0;i<sumCalculators.size();i++){
 297                                 if(sumCalculators[i]->getCols() == 1){
 298                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 299                                         numCols++;
 300                                 }
 301                                 else{
 302                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 303                                         numCols += 3;
 304                                 }
 305                         }
 306                         outputFileHandle << endl;
 307
 308                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 309                         set<string> processedLabels;
 310                         set<string> userLabels = labels;
 311
 312                         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;  }
 313
 314                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 315
 316                                 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;  }
 317
 318                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 319
 320                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 321                                         processedLabels.insert(sabund->getLabel());
 322                                         userLabels.erase(sabund->getLabel());
 323
 324                                         outputFileHandle << sabund->getLabel();
 325                                         for(int i=0;i<sumCalculators.size();i++){
 326                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 327
 328                                                 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;  }
 329
 330                                                 outputFileHandle << '\t';
 331                                                 sumCalculators[i]->print(outputFileHandle);
 332                                         }
 333                                         outputFileHandle << endl;
 334                                         numLines++;
 335                                 }
 336
 337                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 338                                         string saveLabel = sabund->getLabel();
 339
 340                                         delete sabund;
 341                                         sabund = input->getSAbundVector(lastLabel);
 342
 343                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 344                                         processedLabels.insert(sabund->getLabel());
 345                                         userLabels.erase(sabund->getLabel());
 346
 347                                         outputFileHandle << sabund->getLabel();
 348                                         for(int i=0;i<sumCalculators.size();i++){
 349                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 350
 351                                                 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;  }
 352
 353                                                 outputFileHandle << '\t';
 354                                                 sumCalculators[i]->print(outputFileHandle);
 355                                         }
 356                                         outputFileHandle << endl;
 357                                         numLines++;
 358
 359                                         //restore real lastlabel to save below
 360                                         sabund->setLabel(saveLabel);
 361                                 }
 362
 363                                 lastLabel = sabund->getLabel();
 364
 365                                 delete sabund;
 366                                 sabund = input->getSAbundVector();
 367                         }
 368
 369                         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;  }
 370
 371                         //output error messages about any remaining user labels
 372                         set<string>::iterator it;
 373                         bool needToRun = false;
 374                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 375                                 m->mothurOut("Your file does not include the label " + *it);
 376                                 if (processedLabels.count(lastLabel) != 1) {
 377                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 378                                         needToRun = true;
 379                                 }else {
 380                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 381                                 }
 382                         }
 383
 384                         //run last label if you need to
 385                         if (needToRun == true)  {
 386                                 if (sabund != NULL) {   delete sabund;  }
 387                                 sabund = input->getSAbundVector(lastLabel);
 388
 389                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 390                                 outputFileHandle << sabund->getLabel();
 391                                 for(int i=0;i<sumCalculators.size();i++){
 392                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 393
 394                                         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;  }
 395
 396                                         outputFileHandle << '\t';
 397                                         sumCalculators[i]->print(outputFileHandle);
 398                                 }
 399                                 outputFileHandle << endl;
 400                                 numLines++;
 401                                 delete sabund;
 402                         }
 403
 404                         outputFileHandle.close();
 405
 406                         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;  }
 407
 408
 409                         delete input;  globaldata->ginput = NULL;
 410                         delete read;
 411                         delete validCalculator;
 412                         globaldata->sabund = NULL;
 413                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 414                 }
 415
 416                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 417
 418                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 419
 420                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 421                 if ((hadShared != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 422
 423                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 424
 425                 m->mothurOutEndLine();
 426                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 427                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 428                 m->mothurOutEndLine();
 429
 430                 return 0;
 431         }
 432         catch(exception& e) {
 433                 m->errorOut(e, "SummaryCommand", "execute");
 434                 exit(1);
 435         }
 436 }
 437 //**********************************************************************************************************************
 438 vector<string> SummaryCommand::parseSharedFile(string filename) {
 439         try {
 440                 vector<string> filenames;
 441
 442                 map<string, ofstream*> filehandles;
 443                 map<string, ofstream*>::iterator it3;
 444
 445
 446                 //read first line
 447                 read = new ReadOTUFile(filename);
 448                 read->read(&*globaldata);
 449
 450                 input = globaldata->ginput;
 451                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 452
 453                 string sharedFileRoot = m->getRootName(filename);
 454
 455                 //clears file before we start to write to it below
 456                 for (int i=0; i<lookup.size(); i++) {
 457                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 458                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 459                 }
 460
 461                 ofstream* temp;
 462                 for (int i=0; i<lookup.size(); i++) {
 463                         temp = new ofstream;
 464                         filehandles[lookup[i]->getGroup()] = temp;
 465                         groups.push_back(lookup[i]->getGroup());
 466                 }
 467
 468                 while(lookup[0] != NULL) {
 469
 470                         for (int i = 0; i < lookup.size(); i++) {
 471                                 RAbundVector rav = lookup[i]->getRAbundVector();
 472                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 473                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 474                                 (*(filehandles[lookup[i]->getGroup()])).close();
 475                         }
 476
 477                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 478                         lookup = input->getSharedRAbundVectors();
 479                 }
 480
 481                 //free memory
 482                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 483                         delete it3->second;
 484                 }
 485                 delete read;
 486                 delete input;
 487                 globaldata->ginput = NULL;
 488
 489                 return filenames;
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 493                 exit(1);
 494         }
 495 }
 496 //**********************************************************************************************************************
 497 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
 498         try {
 499
 500                 ofstream out;
 501                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
 502
 503                 //open combined file
 504                 m->openOutputFile(combineFileName, out);
 505
 506                 //open each groups summary file
 507                 string newLabel = "";
 508                 map<string, vector<string> > files;
 509                 for (int i=0; i<outputNames.size(); i++) {
 510                         vector<string> thisFilesLines;
 511
 512                         ifstream temp;
 513                         m->openInputFile(outputNames[i], temp);
 514
 515                         //read through first line - labels
 516                         string tempLabel;
 517                         if (i == 0) { //we want to save the labels to output below
 518                                 for (int j = 0; j < numCols+1; j++) {
 519                                         temp >> tempLabel;
 520
 521                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 522                                         }else{  newLabel += tempLabel + '\t';   }
 523                                 }
 524                         }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
 525
 526                         m->gobble(temp);
 527
 528                         //for each label
 529                         for (int k = 0; k < numLines; k++) {
 530
 531                                 string thisLine = "";
 532                                 string tempLabel;
 533
 534                                 for (int j = 0; j < numCols+1; j++) {
 535                                         temp >> tempLabel;
 536
 537                                         //save for later
 538                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 539                                         else{  thisLine += tempLabel + "\t";    }
 540                                 }
 541
 542                                 thisLine += "\n";
 543
 544                                 thisFilesLines.push_back(thisLine);
 545
 546                                 m->gobble(temp);
 547                         }
 548
 549                         files[outputNames[i]] = thisFilesLines;
 550
 551                         temp.close();
 552                         remove(outputNames[i].c_str());
 553                 }
 554
 555                 //output label line to new file
 556                 out << newLabel << endl;
 557
 558                 //for each label
 559                 for (int k = 0; k < numLines; k++) {
 560
 561                         //grab summary data for each group
 562                         for (int i=0; i<outputNames.size(); i++) {
 563                                 out << files[outputNames[i]][k];
 564                         }
 565                 }
 566
 567                 outputNames.clear();
 568
 569                 out.close();
 570
 571                 //return combine file name
 572                 return combineFileName;
 573
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 577                 exit(1);
 578         }
 579 }
 580 //**********************************************************************************************************************