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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 106
 107                 else {
 108                         vector<string> myArray = setParameters();
 109
 110                         OptionParser parser(option);
 111                         map<string,string> parameters = parser.getParameters();
 112                         map<string,string>::iterator it;
 113
 114                         ValidParameters validParameter;
 115
 116                         //check to make sure all parameters are valid for command
 117                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 118                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 119                         }
 120
 121                         //initialize outputTypes
 122                         vector<string> tempOutNames;
 123                         outputTypes["summary"] = tempOutNames;
 124
 125                         //if the user changes the input directory command factory will send this info to us in the output parameter
 126                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 127                         if (inputDir == "not found"){   inputDir = "";          }
 128                         else {
 129                                 string path;
 130                                 it = parameters.find("shared");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 136                                 }
 137
 138                                 it = parameters.find("rabund");
 139                                 //user has given a template file
 140                                 if(it != parameters.end()){
 141                                         path = m->hasPath(it->second);
 142                                         //if the user has not given a path then, add inputdir. else leave path alone.
 143                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 144                                 }
 145
 146                                 it = parameters.find("sabund");
 147                                 //user has given a template file
 148                                 if(it != parameters.end()){
 149                                         path = m->hasPath(it->second);
 150                                         //if the user has not given a path then, add inputdir. else leave path alone.
 151                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 152                                 }
 153
 154                                 it = parameters.find("list");
 155                                 //user has given a template file
 156                                 if(it != parameters.end()){
 157                                         path = m->hasPath(it->second);
 158                                         //if the user has not given a path then, add inputdir. else leave path alone.
 159                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 160                                 }
 161                         }
 162
 163                         //check for required parameters
 164                         listfile = validParameter.validFile(parameters, "list", true);
 165                         if (listfile == "not open") { listfile = ""; abort = true; }
 166                         else if (listfile == "not found") { listfile = ""; }
 167                         else {  format = "list"; inputfile = listfile; }
 168
 169                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 170                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 171                         else if (sabundfile == "not found") { sabundfile = ""; }
 172                         else {  format = "sabund"; inputfile = sabundfile; }
 173
 174                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 175                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 176                         else if (rabundfile == "not found") { rabundfile = ""; }
 177                         else {  format = "rabund"; inputfile = rabundfile; }
 178
 179                         sharedfile = validParameter.validFile(parameters, "shared", true);
 180                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 181                         else if (sharedfile == "not found") { sharedfile = ""; }
 182                         else {  format = "sharedfile"; inputfile = sharedfile; }
 183
 184                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 185                                 //is there are current file available for any of these?
 186                                 //give priority to shared, then list, then rabund, then sabund
 187                                 //if there is a current shared file, use it
 188                                 sharedfile = m->getSharedFile();
 189                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 190                                 else {
 191                                         listfile = m->getListFile();
 192                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 193                                         else {
 194                                                 rabundfile = m->getRabundFile();
 195                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 196                                                 else {
 197                                                         sabundfile = m->getSabundFile();
 198                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 199                                                         else {
 200                                                                 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();
 201                                                                 abort = true;
 202                                                         }
 203                                                 }
 204                                         }
 205                                 }
 206                         }
 207
 208                         //if the user changes the output directory command factory will send this info to us in the output parameter
 209                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 210
 211                         //check for optional parameter and set defaults
 212                         // ...at some point should added some additional type checking...
 213                         label = validParameter.validFile(parameters, "label", false);
 214                         if (label == "not found") { label = ""; }
 215                         else {
 216                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 217                                 else { allLines = 1;  }
 218                         }
 219
 220                         calc = validParameter.validFile(parameters, "calc", false);
 221                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 222                         else {
 223                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 224                         }
 225                         m->splitAtDash(calc, Estimators);
 226
 227                         string temp;
 228                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 229                         convert(temp, abund);
 230
 231                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 232                         convert(temp, size);
 233
 234                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 235                         groupMode = m->isTrue(temp);
 236
 237
 238                 }
 239         }
 240         catch(exception& e) {
 241                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 242                 exit(1);
 243         }
 244 }
 245 //**********************************************************************************************************************
 246
 247 int SummaryCommand::execute(){
 248         try {
 249
 250                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 251
 252                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 253                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 254
 255                 if (m->control_pressed) { return 0; }
 256
 257                 int numLines = 0;
 258                 int numCols = 0;
 259
 260                 for (int p = 0; p < inputFileNames.size(); p++) {
 261
 262                         numLines = 0;
 263                         numCols = 0;
 264
 265                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 266                         outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
 267
 268                         if (inputFileNames.size() > 1) {
 269                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 270                         }
 271
 272                         sumCalculators.clear();
 273
 274                         ValidCalculators validCalculator;
 275
 276                         for (int i=0; i<Estimators.size(); i++) {
 277                                 if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
 278                                         if(Estimators[i] == "sobs"){
 279                                                 sumCalculators.push_back(new Sobs());
 280                                         }else if(Estimators[i] == "chao"){
 281                                                 sumCalculators.push_back(new Chao1());
 282                                         }else if(Estimators[i] == "coverage"){
 283                                                 sumCalculators.push_back(new Coverage());
 284                                         }else if(Estimators[i] == "geometric"){
 285                                                 sumCalculators.push_back(new Geom());
 286                                         }else if(Estimators[i] == "logseries"){
 287                                                 sumCalculators.push_back(new LogSD());
 288                                         }else if(Estimators[i] == "qstat"){
 289                                                 sumCalculators.push_back(new QStat());
 290                                         }else if(Estimators[i] == "bergerparker"){
 291                                                 sumCalculators.push_back(new BergerParker());
 292                                         }else if(Estimators[i] == "bstick"){
 293                                                 sumCalculators.push_back(new BStick());
 294                                         }else if(Estimators[i] == "ace"){
 295                                                 if(abund < 5)
 296                                                         abund = 10;
 297                                                 sumCalculators.push_back(new Ace(abund));
 298                                         }else if(Estimators[i] == "jack"){
 299                                                 sumCalculators.push_back(new Jackknife());
 300                                         }else if(Estimators[i] == "shannon"){
 301                                                 sumCalculators.push_back(new Shannon());
 302                                         }else if(Estimators[i] == "shannoneven"){
 303                                                 sumCalculators.push_back(new ShannonEven());
 304                                         }else if(Estimators[i] == "npshannon"){
 305                                                 sumCalculators.push_back(new NPShannon());
 306                                         }else if(Estimators[i] == "heip"){
 307                                                 sumCalculators.push_back(new Heip());
 308                                         }else if(Estimators[i] == "smithwilson"){
 309                                                 sumCalculators.push_back(new SmithWilson());
 310                                         }else if(Estimators[i] == "simpson"){
 311                                                 sumCalculators.push_back(new Simpson());
 312                                         }else if(Estimators[i] == "simpsoneven"){
 313                                                 sumCalculators.push_back(new SimpsonEven());
 314                                         }else if(Estimators[i] == "invsimpson"){
 315                                                 sumCalculators.push_back(new InvSimpson());
 316                                         }else if(Estimators[i] == "bootstrap"){
 317                                                 sumCalculators.push_back(new Bootstrap());
 318                                         }else if (Estimators[i] == "nseqs") {
 319                                                 sumCalculators.push_back(new NSeqs());
 320                                         }else if (Estimators[i] == "goodscoverage") {
 321                                                 sumCalculators.push_back(new GoodsCoverage());
 322                                         }else if (Estimators[i] == "efron") {
 323                                                 sumCalculators.push_back(new Efron(size));
 324                                         }else if (Estimators[i] == "boneh") {
 325                                                 sumCalculators.push_back(new Boneh(size));
 326                                         }else if (Estimators[i] == "solow") {
 327                                                 sumCalculators.push_back(new Solow(size));
 328                                         }else if (Estimators[i] == "shen") {
 329                                                 sumCalculators.push_back(new Shen(size, abund));
 330                                         }
 331                                 }
 332                         }
 333
 334                         //if the users entered no valid calculators don't execute command
 335                         if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
 336
 337                         ofstream outputFileHandle;
 338                         m->openOutputFile(fileNameRoot, outputFileHandle);
 339                         outputFileHandle << "label";
 340
 341                         input = new InputData(inputFileNames[p], format);
 342                         sabund = input->getSAbundVector();
 343                         string lastLabel = sabund->getLabel();
 344
 345                         for(int i=0;i<sumCalculators.size();i++){
 346                                 if(sumCalculators[i]->getCols() == 1){
 347                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 348                                         numCols++;
 349                                 }
 350                                 else{
 351                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 352                                         numCols += 3;
 353                                 }
 354                         }
 355                         outputFileHandle << endl;
 356
 357                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 358                         set<string> processedLabels;
 359                         set<string> userLabels = labels;
 360
 361                         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;  }
 362
 363                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 364
 365                                 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;  }
 366
 367                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 368
 369                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 370                                         processedLabels.insert(sabund->getLabel());
 371                                         userLabels.erase(sabund->getLabel());
 372
 373                                         outputFileHandle << sabund->getLabel();
 374                                         for(int i=0;i<sumCalculators.size();i++){
 375                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 376
 377                                                 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;  }
 378
 379                                                 outputFileHandle << '\t';
 380                                                 sumCalculators[i]->print(outputFileHandle);
 381                                         }
 382                                         outputFileHandle << endl;
 383                                         numLines++;
 384                                 }
 385
 386                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 387                                         string saveLabel = sabund->getLabel();
 388
 389                                         delete sabund;
 390                                         sabund = input->getSAbundVector(lastLabel);
 391
 392                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 393                                         processedLabels.insert(sabund->getLabel());
 394                                         userLabels.erase(sabund->getLabel());
 395
 396                                         outputFileHandle << sabund->getLabel();
 397                                         for(int i=0;i<sumCalculators.size();i++){
 398                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 399
 400                                                 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;  }
 401
 402                                                 outputFileHandle << '\t';
 403                                                 sumCalculators[i]->print(outputFileHandle);
 404                                         }
 405                                         outputFileHandle << endl;
 406                                         numLines++;
 407
 408                                         //restore real lastlabel to save below
 409                                         sabund->setLabel(saveLabel);
 410                                 }
 411
 412                                 lastLabel = sabund->getLabel();
 413
 414                                 delete sabund;
 415                                 sabund = input->getSAbundVector();
 416                         }
 417
 418                         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;  }
 419
 420                         //output error messages about any remaining user labels
 421                         set<string>::iterator it;
 422                         bool needToRun = false;
 423                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 424                                 m->mothurOut("Your file does not include the label " + *it);
 425                                 if (processedLabels.count(lastLabel) != 1) {
 426                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 427                                         needToRun = true;
 428                                 }else {
 429                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 430                                 }
 431                         }
 432
 433                         //run last label if you need to
 434                         if (needToRun == true)  {
 435                                 if (sabund != NULL) {   delete sabund;  }
 436                                 sabund = input->getSAbundVector(lastLabel);
 437
 438                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 439                                 outputFileHandle << sabund->getLabel();
 440                                 for(int i=0;i<sumCalculators.size();i++){
 441                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 442
 443                                         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;  }
 444
 445                                         outputFileHandle << '\t';
 446                                         sumCalculators[i]->print(outputFileHandle);
 447                                 }
 448                                 outputFileHandle << endl;
 449                                 numLines++;
 450                                 delete sabund;
 451                         }
 452
 453                         outputFileHandle.close();
 454
 455                         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;  }
 456
 457
 458                         delete input;
 459                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 460                 }
 461
 462                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 463
 464                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 465                 if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 466
 467                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 468
 469                 m->mothurOutEndLine();
 470                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 471                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 472                 m->mothurOutEndLine();
 473
 474                 return 0;
 475         }
 476         catch(exception& e) {
 477                 m->errorOut(e, "SummaryCommand", "execute");
 478                 exit(1);
 479         }
 480 }
 481 //**********************************************************************************************************************
 482 vector<string> SummaryCommand::parseSharedFile(string filename) {
 483         try {
 484                 vector<string> filenames;
 485
 486                 map<string, ofstream*> filehandles;
 487                 map<string, ofstream*>::iterator it3;
 488
 489                 input = new InputData(filename, "sharedfile");
 490                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 491
 492                 string sharedFileRoot = m->getRootName(filename);
 493
 494                 //clears file before we start to write to it below
 495                 for (int i=0; i<lookup.size(); i++) {
 496                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 497                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 498                 }
 499
 500                 ofstream* temp;
 501                 for (int i=0; i<lookup.size(); i++) {
 502                         temp = new ofstream;
 503                         filehandles[lookup[i]->getGroup()] = temp;
 504                         groups.push_back(lookup[i]->getGroup());
 505                 }
 506
 507                 while(lookup[0] != NULL) {
 508
 509                         for (int i = 0; i < lookup.size(); i++) {
 510                                 RAbundVector rav = lookup[i]->getRAbundVector();
 511                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 512                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 513                                 (*(filehandles[lookup[i]->getGroup()])).close();
 514                         }
 515
 516                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 517                         lookup = input->getSharedRAbundVectors();
 518                 }
 519
 520                 //free memory
 521                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 522                         delete it3->second;
 523                 }
 524
 525                 delete input;
 526
 527                 return filenames;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 531                 exit(1);
 532         }
 533 }
 534 //**********************************************************************************************************************
 535 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
 536         try {
 537
 538                 ofstream out;
 539                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
 540
 541                 //open combined file
 542                 m->openOutputFile(combineFileName, out);
 543
 544                 //open each groups summary file
 545                 string newLabel = "";
 546                 map<string, vector<string> > files;
 547                 for (int i=0; i<outputNames.size(); i++) {
 548                         vector<string> thisFilesLines;
 549
 550                         ifstream temp;
 551                         m->openInputFile(outputNames[i], temp);
 552
 553                         //read through first line - labels
 554                         string tempLabel;
 555                         if (i == 0) { //we want to save the labels to output below
 556                                 for (int j = 0; j < numCols+1; j++) {
 557                                         temp >> tempLabel;
 558
 559                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 560                                         }else{  newLabel += tempLabel + '\t';   }
 561                                 }
 562                         }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
 563
 564                         m->gobble(temp);
 565
 566                         //for each label
 567                         for (int k = 0; k < numLines; k++) {
 568
 569                                 string thisLine = "";
 570                                 string tempLabel;
 571
 572                                 for (int j = 0; j < numCols+1; j++) {
 573                                         temp >> tempLabel;
 574
 575                                         //save for later
 576                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 577                                         else{  thisLine += tempLabel + "\t";    }
 578                                 }
 579
 580                                 thisLine += "\n";
 581
 582                                 thisFilesLines.push_back(thisLine);
 583
 584                                 m->gobble(temp);
 585                         }
 586
 587                         files[outputNames[i]] = thisFilesLines;
 588
 589                         temp.close();
 590                         remove(outputNames[i].c_str());
 591                 }
 592
 593                 //output label line to new file
 594                 out << newLabel << endl;
 595
 596                 //for each label
 597                 for (int k = 0; k < numLines; k++) {
 598
 599                         //grab summary data for each group
 600                         for (int i=0; i<outputNames.size(); i++) {
 601                                 out << files[outputNames[i]][k];
 602                         }
 603                 }
 604
 605                 outputNames.clear();
 606
 607                 out.close();
 608
 609                 //return combine file name
 610                 return combineFileName;
 611
 612         }
 613         catch(exception& e) {
 614                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 615                 exit(1);
 616         }
 617 }
 618 //**********************************************************************************************************************