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::setParameters(){
  39         try {
  40                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  41                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  42                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  43                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  44                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  45                 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
  46                 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
  47                 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
  48                 CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
  49                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  50                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  51
  52                 vector<string> myArray;
  53                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "SummaryCommand", "setParameters");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string SummaryCommand::getHelpString(){
  63         try {
  64                 string helpString = "";
  65                 ValidCalculators validCalculator;
  66                 helpString += "The summary.single command parameters are list, sabund, rabund, shared, label, calc, abund and groupmode.  list, sabund, rabund or shared is required unless you have a valid current file.\n";
  67                 helpString += "The summary.single command should be in the following format: \n";
  68                 helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
  69                 helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
  70                 helpString += validCalculator.printCalc("summary");
  71                 helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
  72                 helpString += "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";
  73                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  74                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
  75                 return helpString;
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "SummaryCommand", "getHelpString");
  79                 exit(1);
  80         }
  81 }
  82
  83 //**********************************************************************************************************************
  84 SummaryCommand::SummaryCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["summary"] = tempOutNames;
  90         }
  91         catch(exception& e) {
  92                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
  93                 exit(1);
  94         }
  95 }
  96 //**********************************************************************************************************************
  97
  98 SummaryCommand::SummaryCommand(string option)  {
  99         try {
 100                 abort = false; calledHelp = false;
 101                 allLines = 1;
 102
 103                 //allow user to run help
 104                 if(option == "help") {  help();  abort = true; calledHelp = true; }
 105
 106                 else {
 107                         vector<string> myArray = setParameters();
 108
 109                         OptionParser parser(option);
 110                         map<string,string> parameters = parser.getParameters();
 111                         map<string,string>::iterator it;
 112
 113                         ValidParameters validParameter;
 114
 115                         //check to make sure all parameters are valid for command
 116                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 117                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 118                         }
 119
 120                         //initialize outputTypes
 121                         vector<string> tempOutNames;
 122                         outputTypes["summary"] = tempOutNames;
 123
 124                         //if the user changes the input directory command factory will send this info to us in the output parameter
 125                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 126                         if (inputDir == "not found"){   inputDir = "";          }
 127                         else {
 128                                 string path;
 129                                 it = parameters.find("shared");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 135                                 }
 136
 137                                 it = parameters.find("rabund");
 138                                 //user has given a template file
 139                                 if(it != parameters.end()){
 140                                         path = m->hasPath(it->second);
 141                                         //if the user has not given a path then, add inputdir. else leave path alone.
 142                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 143                                 }
 144
 145                                 it = parameters.find("sabund");
 146                                 //user has given a template file
 147                                 if(it != parameters.end()){
 148                                         path = m->hasPath(it->second);
 149                                         //if the user has not given a path then, add inputdir. else leave path alone.
 150                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 151                                 }
 152
 153                                 it = parameters.find("list");
 154                                 //user has given a template file
 155                                 if(it != parameters.end()){
 156                                         path = m->hasPath(it->second);
 157                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 159                                 }
 160                         }
 161
 162                         //check for required parameters
 163                         listfile = validParameter.validFile(parameters, "list", true);
 164                         if (listfile == "not open") { listfile = ""; abort = true; }
 165                         else if (listfile == "not found") { listfile = ""; }
 166                         else {  format = "list"; inputfile = listfile; }
 167
 168                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 169                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 170                         else if (sabundfile == "not found") { sabundfile = ""; }
 171                         else {  format = "sabund"; inputfile = sabundfile; }
 172
 173                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 174                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 175                         else if (rabundfile == "not found") { rabundfile = ""; }
 176                         else {  format = "rabund"; inputfile = rabundfile; }
 177
 178                         sharedfile = validParameter.validFile(parameters, "shared", true);
 179                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 180                         else if (sharedfile == "not found") { sharedfile = ""; }
 181                         else {  format = "sharedfile"; inputfile = sharedfile; }
 182
 183                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 184                                 //is there are current file available for any of these?
 185                                 //give priority to shared, then list, then rabund, then sabund
 186                                 //if there is a current shared file, use it
 187                                 sharedfile = m->getSharedFile();
 188                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 189                                 else {
 190                                         listfile = m->getListFile();
 191                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 192                                         else {
 193                                                 rabundfile = m->getRabundFile();
 194                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 195                                                 else {
 196                                                         sabundfile = m->getSabundFile();
 197                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 198                                                         else {
 199                                                                 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
 200                                                                 abort = true;
 201                                                         }
 202                                                 }
 203                                         }
 204                                 }
 205                         }
 206
 207                         //if the user changes the output directory command factory will send this info to us in the output parameter
 208                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 209
 210                         //check for optional parameter and set defaults
 211                         // ...at some point should added some additional type checking...
 212                         label = validParameter.validFile(parameters, "label", false);
 213                         if (label == "not found") { label = ""; }
 214                         else {
 215                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 216                                 else { allLines = 1;  }
 217                         }
 218
 219                         calc = validParameter.validFile(parameters, "calc", false);
 220                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 221                         else {
 222                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 223                         }
 224                         m->splitAtDash(calc, Estimators);
 225
 226                         string temp;
 227                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 228                         convert(temp, abund);
 229
 230                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 231                         convert(temp, size);
 232
 233                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 234                         groupMode = m->isTrue(temp);
 235
 236
 237                 }
 238         }
 239         catch(exception& e) {
 240                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 241                 exit(1);
 242         }
 243 }
 244 //**********************************************************************************************************************
 245
 246 int SummaryCommand::execute(){
 247         try {
 248
 249                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 250
 251                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 252                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 253
 254                 if (m->control_pressed) { return 0; }
 255
 256                 int numLines = 0;
 257                 int numCols = 0;
 258
 259                 for (int p = 0; p < inputFileNames.size(); p++) {
 260
 261                         numLines = 0;
 262                         numCols = 0;
 263
 264                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 265                         outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
 266
 267                         if (inputFileNames.size() > 1) {
 268                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 269                         }
 270
 271                         sumCalculators.clear();
 272
 273                         ValidCalculators validCalculator;
 274
 275                         for (int i=0; i<Estimators.size(); i++) {
 276                                 if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
 277                                         if(Estimators[i] == "sobs"){
 278                                                 sumCalculators.push_back(new Sobs());
 279                                         }else if(Estimators[i] == "chao"){
 280                                                 sumCalculators.push_back(new Chao1());
 281                                         }else if(Estimators[i] == "coverage"){
 282                                                 sumCalculators.push_back(new Coverage());
 283                                         }else if(Estimators[i] == "geometric"){
 284                                                 sumCalculators.push_back(new Geom());
 285                                         }else if(Estimators[i] == "logseries"){
 286                                                 sumCalculators.push_back(new LogSD());
 287                                         }else if(Estimators[i] == "qstat"){
 288                                                 sumCalculators.push_back(new QStat());
 289                                         }else if(Estimators[i] == "bergerparker"){
 290                                                 sumCalculators.push_back(new BergerParker());
 291                                         }else if(Estimators[i] == "bstick"){
 292                                                 sumCalculators.push_back(new BStick());
 293                                         }else if(Estimators[i] == "ace"){
 294                                                 if(abund < 5)
 295                                                         abund = 10;
 296                                                 sumCalculators.push_back(new Ace(abund));
 297                                         }else if(Estimators[i] == "jack"){
 298                                                 sumCalculators.push_back(new Jackknife());
 299                                         }else if(Estimators[i] == "shannon"){
 300                                                 sumCalculators.push_back(new Shannon());
 301                                         }else if(Estimators[i] == "shannoneven"){
 302                                                 sumCalculators.push_back(new ShannonEven());
 303                                         }else if(Estimators[i] == "npshannon"){
 304                                                 sumCalculators.push_back(new NPShannon());
 305                                         }else if(Estimators[i] == "heip"){
 306                                                 sumCalculators.push_back(new Heip());
 307                                         }else if(Estimators[i] == "smithwilson"){
 308                                                 sumCalculators.push_back(new SmithWilson());
 309                                         }else if(Estimators[i] == "simpson"){
 310                                                 sumCalculators.push_back(new Simpson());
 311                                         }else if(Estimators[i] == "simpsoneven"){
 312                                                 sumCalculators.push_back(new SimpsonEven());
 313                                         }else if(Estimators[i] == "invsimpson"){
 314                                                 sumCalculators.push_back(new InvSimpson());
 315                                         }else if(Estimators[i] == "bootstrap"){
 316                                                 sumCalculators.push_back(new Bootstrap());
 317                                         }else if (Estimators[i] == "nseqs") {
 318                                                 sumCalculators.push_back(new NSeqs());
 319                                         }else if (Estimators[i] == "goodscoverage") {
 320                                                 sumCalculators.push_back(new GoodsCoverage());
 321                                         }else if (Estimators[i] == "efron") {
 322                                                 sumCalculators.push_back(new Efron(size));
 323                                         }else if (Estimators[i] == "boneh") {
 324                                                 sumCalculators.push_back(new Boneh(size));
 325                                         }else if (Estimators[i] == "solow") {
 326                                                 sumCalculators.push_back(new Solow(size));
 327                                         }else if (Estimators[i] == "shen") {
 328                                                 sumCalculators.push_back(new Shen(size, abund));
 329                                         }
 330                                 }
 331                         }
 332
 333                         //if the users entered no valid calculators don't execute command
 334                         if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
 335
 336                         ofstream outputFileHandle;
 337                         m->openOutputFile(fileNameRoot, outputFileHandle);
 338                         outputFileHandle << "label";
 339
 340                         input = new InputData(inputFileNames[p], format);
 341                         sabund = input->getSAbundVector();
 342                         string lastLabel = sabund->getLabel();
 343
 344                         for(int i=0;i<sumCalculators.size();i++){
 345                                 if(sumCalculators[i]->getCols() == 1){
 346                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 347                                         numCols++;
 348                                 }
 349                                 else{
 350                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 351                                         numCols += 3;
 352                                 }
 353                         }
 354                         outputFileHandle << endl;
 355
 356                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 357                         set<string> processedLabels;
 358                         set<string> userLabels = labels;
 359
 360                         if (m->control_pressed) {  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 sabund;  delete input;  return 0;  }
 361
 362                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 363
 364                                 if (m->control_pressed) { 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 sabund;  delete input;  return 0;  }
 365
 366                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 367
 368                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 369                                         processedLabels.insert(sabund->getLabel());
 370                                         userLabels.erase(sabund->getLabel());
 371
 372                                         outputFileHandle << sabund->getLabel();
 373                                         for(int i=0;i<sumCalculators.size();i++){
 374                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 375
 376                                                 if (m->control_pressed) { 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 sabund;  delete input;  return 0;  }
 377
 378                                                 outputFileHandle << '\t';
 379                                                 sumCalculators[i]->print(outputFileHandle);
 380                                         }
 381                                         outputFileHandle << endl;
 382                                         numLines++;
 383                                 }
 384
 385                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 386                                         string saveLabel = sabund->getLabel();
 387
 388                                         delete sabund;
 389                                         sabund = input->getSAbundVector(lastLabel);
 390
 391                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 392                                         processedLabels.insert(sabund->getLabel());
 393                                         userLabels.erase(sabund->getLabel());
 394
 395                                         outputFileHandle << sabund->getLabel();
 396                                         for(int i=0;i<sumCalculators.size();i++){
 397                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 398
 399                                                 if (m->control_pressed) {  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 sabund;  delete input;  return 0;  }
 400
 401                                                 outputFileHandle << '\t';
 402                                                 sumCalculators[i]->print(outputFileHandle);
 403                                         }
 404                                         outputFileHandle << endl;
 405                                         numLines++;
 406
 407                                         //restore real lastlabel to save below
 408                                         sabund->setLabel(saveLabel);
 409                                 }
 410
 411                                 lastLabel = sabund->getLabel();
 412
 413                                 delete sabund;
 414                                 sabund = input->getSAbundVector();
 415                         }
 416
 417                         if (m->control_pressed) {  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 input;  return 0;  }
 418
 419                         //output error messages about any remaining user labels
 420                         set<string>::iterator it;
 421                         bool needToRun = false;
 422                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 423                                 m->mothurOut("Your file does not include the label " + *it);
 424                                 if (processedLabels.count(lastLabel) != 1) {
 425                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 426                                         needToRun = true;
 427                                 }else {
 428                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 429                                 }
 430                         }
 431
 432                         //run last label if you need to
 433                         if (needToRun == true)  {
 434                                 if (sabund != NULL) {   delete sabund;  }
 435                                 sabund = input->getSAbundVector(lastLabel);
 436
 437                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 438                                 outputFileHandle << sabund->getLabel();
 439                                 for(int i=0;i<sumCalculators.size();i++){
 440                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 441
 442                                         if (m->control_pressed) {  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 sabund;  delete input; return 0;  }
 443
 444                                         outputFileHandle << '\t';
 445                                         sumCalculators[i]->print(outputFileHandle);
 446                                 }
 447                                 outputFileHandle << endl;
 448                                 numLines++;
 449                                 delete sabund;
 450                         }
 451
 452                         outputFileHandle.close();
 453
 454                         if (m->control_pressed) {  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 input;  return 0;  }
 455
 456
 457                         delete input;
 458                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 459                 }
 460
 461                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 462
 463                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 464                 if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 465
 466                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 467
 468                 m->mothurOutEndLine();
 469                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 470                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 471                 m->mothurOutEndLine();
 472
 473                 return 0;
 474         }
 475         catch(exception& e) {
 476                 m->errorOut(e, "SummaryCommand", "execute");
 477                 exit(1);
 478         }
 479 }
 480 //**********************************************************************************************************************
 481 vector<string> SummaryCommand::parseSharedFile(string filename) {
 482         try {
 483                 vector<string> filenames;
 484
 485                 map<string, ofstream*> filehandles;
 486                 map<string, ofstream*>::iterator it3;
 487
 488                 input = new InputData(filename, "sharedfile");
 489                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 490
 491                 string sharedFileRoot = m->getRootName(filename);
 492
 493                 //clears file before we start to write to it below
 494                 for (int i=0; i<lookup.size(); i++) {
 495                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 496                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 497                 }
 498
 499                 ofstream* temp;
 500                 for (int i=0; i<lookup.size(); i++) {
 501                         temp = new ofstream;
 502                         filehandles[lookup[i]->getGroup()] = temp;
 503                         groups.push_back(lookup[i]->getGroup());
 504                 }
 505
 506                 while(lookup[0] != NULL) {
 507
 508                         for (int i = 0; i < lookup.size(); i++) {
 509                                 RAbundVector rav = lookup[i]->getRAbundVector();
 510                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 511                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 512                                 (*(filehandles[lookup[i]->getGroup()])).close();
 513                         }
 514
 515                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 516                         lookup = input->getSharedRAbundVectors();
 517                 }
 518
 519                 //free memory
 520                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 521                         delete it3->second;
 522                 }
 523
 524                 delete input;
 525
 526                 return filenames;
 527         }
 528         catch(exception& e) {
 529                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 530                 exit(1);
 531         }
 532 }
 533 //**********************************************************************************************************************
 534 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
 535         try {
 536
 537                 ofstream out;
 538                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
 539
 540                 //open combined file
 541                 m->openOutputFile(combineFileName, out);
 542
 543                 //open each groups summary file
 544                 string newLabel = "";
 545                 map<string, vector<string> > files;
 546                 for (int i=0; i<outputNames.size(); i++) {
 547                         vector<string> thisFilesLines;
 548
 549                         ifstream temp;
 550                         m->openInputFile(outputNames[i], temp);
 551
 552                         //read through first line - labels
 553                         string tempLabel;
 554                         if (i == 0) { //we want to save the labels to output below
 555                                 for (int j = 0; j < numCols+1; j++) {
 556                                         temp >> tempLabel;
 557
 558                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 559                                         }else{  newLabel += tempLabel + '\t';   }
 560                                 }
 561                         }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
 562
 563                         m->gobble(temp);
 564
 565                         //for each label
 566                         for (int k = 0; k < numLines; k++) {
 567
 568                                 string thisLine = "";
 569                                 string tempLabel;
 570
 571                                 for (int j = 0; j < numCols+1; j++) {
 572                                         temp >> tempLabel;
 573
 574                                         //save for later
 575                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 576                                         else{  thisLine += tempLabel + "\t";    }
 577                                 }
 578
 579                                 thisLine += "\n";
 580
 581                                 thisFilesLines.push_back(thisLine);
 582
 583                                 m->gobble(temp);
 584                         }
 585
 586                         files[outputNames[i]] = thisFilesLines;
 587
 588                         temp.close();
 589                         remove(outputNames[i].c_str());
 590                 }
 591
 592                 //output label line to new file
 593                 out << newLabel << endl;
 594
 595                 //for each label
 596                 for (int k = 0; k < numLines; k++) {
 597
 598                         //grab summary data for each group
 599                         for (int i=0; i<outputNames.size(); i++) {
 600                                 out << files[outputNames[i]][k];
 601                         }
 602                 }
 603
 604                 outputNames.clear();
 605
 606                 out.close();
 607
 608                 //return combine file name
 609                 return combineFileName;
 610
 611         }
 612         catch(exception& e) {
 613                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 614                 exit(1);
 615         }
 616 }
 617 //**********************************************************************************************************************