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                         if (m->inUsersGroups("citation", Estimators)) {
 227                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 228                                 //remove citation from list of calcs
 229                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 230                         }
 231
 232                         string temp;
 233                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 234                         convert(temp, abund);
 235
 236                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 237                         convert(temp, size);
 238
 239                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 240                         groupMode = m->isTrue(temp);
 241
 242
 243                 }
 244         }
 245         catch(exception& e) {
 246                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 247                 exit(1);
 248         }
 249 }
 250 //**********************************************************************************************************************
 251
 252 int SummaryCommand::execute(){
 253         try {
 254
 255                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 256
 257                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 258                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 259
 260                 if (m->control_pressed) { return 0; }
 261
 262                 int numLines = 0;
 263                 int numCols = 0;
 264
 265                 for (int p = 0; p < inputFileNames.size(); p++) {
 266
 267                         numLines = 0;
 268                         numCols = 0;
 269
 270                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 271                         outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
 272
 273                         if (inputFileNames.size() > 1) {
 274                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 275                         }
 276
 277                         sumCalculators.clear();
 278
 279                         ValidCalculators validCalculator;
 280
 281                         for (int i=0; i<Estimators.size(); i++) {
 282                                 if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
 283                                         if(Estimators[i] == "sobs"){
 284                                                 sumCalculators.push_back(new Sobs());
 285                                         }else if(Estimators[i] == "chao"){
 286                                                 sumCalculators.push_back(new Chao1());
 287                                         }else if(Estimators[i] == "coverage"){
 288                                                 sumCalculators.push_back(new Coverage());
 289                                         }else if(Estimators[i] == "geometric"){
 290                                                 sumCalculators.push_back(new Geom());
 291                                         }else if(Estimators[i] == "logseries"){
 292                                                 sumCalculators.push_back(new LogSD());
 293                                         }else if(Estimators[i] == "qstat"){
 294                                                 sumCalculators.push_back(new QStat());
 295                                         }else if(Estimators[i] == "bergerparker"){
 296                                                 sumCalculators.push_back(new BergerParker());
 297                                         }else if(Estimators[i] == "bstick"){
 298                                                 sumCalculators.push_back(new BStick());
 299                                         }else if(Estimators[i] == "ace"){
 300                                                 if(abund < 5)
 301                                                         abund = 10;
 302                                                 sumCalculators.push_back(new Ace(abund));
 303                                         }else if(Estimators[i] == "jack"){
 304                                                 sumCalculators.push_back(new Jackknife());
 305                                         }else if(Estimators[i] == "shannon"){
 306                                                 sumCalculators.push_back(new Shannon());
 307                                         }else if(Estimators[i] == "shannoneven"){
 308                                                 sumCalculators.push_back(new ShannonEven());
 309                                         }else if(Estimators[i] == "npshannon"){
 310                                                 sumCalculators.push_back(new NPShannon());
 311                                         }else if(Estimators[i] == "heip"){
 312                                                 sumCalculators.push_back(new Heip());
 313                                         }else if(Estimators[i] == "smithwilson"){
 314                                                 sumCalculators.push_back(new SmithWilson());
 315                                         }else if(Estimators[i] == "simpson"){
 316                                                 sumCalculators.push_back(new Simpson());
 317                                         }else if(Estimators[i] == "simpsoneven"){
 318                                                 sumCalculators.push_back(new SimpsonEven());
 319                                         }else if(Estimators[i] == "invsimpson"){
 320                                                 sumCalculators.push_back(new InvSimpson());
 321                                         }else if(Estimators[i] == "bootstrap"){
 322                                                 sumCalculators.push_back(new Bootstrap());
 323                                         }else if (Estimators[i] == "nseqs") {
 324                                                 sumCalculators.push_back(new NSeqs());
 325                                         }else if (Estimators[i] == "goodscoverage") {
 326                                                 sumCalculators.push_back(new GoodsCoverage());
 327                                         }else if (Estimators[i] == "efron") {
 328                                                 sumCalculators.push_back(new Efron(size));
 329                                         }else if (Estimators[i] == "boneh") {
 330                                                 sumCalculators.push_back(new Boneh(size));
 331                                         }else if (Estimators[i] == "solow") {
 332                                                 sumCalculators.push_back(new Solow(size));
 333                                         }else if (Estimators[i] == "shen") {
 334                                                 sumCalculators.push_back(new Shen(size, abund));
 335                                         }
 336                                 }
 337                         }
 338
 339                         //if the users entered no valid calculators don't execute command
 340                         if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
 341
 342                         ofstream outputFileHandle;
 343                         m->openOutputFile(fileNameRoot, outputFileHandle);
 344                         outputFileHandle << "label";
 345
 346                         input = new InputData(inputFileNames[p], format);
 347                         sabund = input->getSAbundVector();
 348                         string lastLabel = sabund->getLabel();
 349
 350                         for(int i=0;i<sumCalculators.size();i++){
 351                                 if(sumCalculators[i]->getCols() == 1){
 352                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 353                                         numCols++;
 354                                 }
 355                                 else{
 356                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 357                                         numCols += 3;
 358                                 }
 359                         }
 360                         outputFileHandle << endl;
 361
 362                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 363                         set<string> processedLabels;
 364                         set<string> userLabels = labels;
 365
 366                         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;  }
 367
 368                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 369
 370                                 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;  }
 371
 372                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 373
 374                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 375                                         processedLabels.insert(sabund->getLabel());
 376                                         userLabels.erase(sabund->getLabel());
 377
 378                                         outputFileHandle << sabund->getLabel();
 379                                         for(int i=0;i<sumCalculators.size();i++){
 380                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 381
 382                                                 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;  }
 383
 384                                                 outputFileHandle << '\t';
 385                                                 sumCalculators[i]->print(outputFileHandle);
 386                                         }
 387                                         outputFileHandle << endl;
 388                                         numLines++;
 389                                 }
 390
 391                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 392                                         string saveLabel = sabund->getLabel();
 393
 394                                         delete sabund;
 395                                         sabund = input->getSAbundVector(lastLabel);
 396
 397                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 398                                         processedLabels.insert(sabund->getLabel());
 399                                         userLabels.erase(sabund->getLabel());
 400
 401                                         outputFileHandle << sabund->getLabel();
 402                                         for(int i=0;i<sumCalculators.size();i++){
 403                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 404
 405                                                 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;  }
 406
 407                                                 outputFileHandle << '\t';
 408                                                 sumCalculators[i]->print(outputFileHandle);
 409                                         }
 410                                         outputFileHandle << endl;
 411                                         numLines++;
 412
 413                                         //restore real lastlabel to save below
 414                                         sabund->setLabel(saveLabel);
 415                                 }
 416
 417                                 lastLabel = sabund->getLabel();
 418
 419                                 delete sabund;
 420                                 sabund = input->getSAbundVector();
 421                         }
 422
 423                         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;  }
 424
 425                         //output error messages about any remaining user labels
 426                         set<string>::iterator it;
 427                         bool needToRun = false;
 428                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 429                                 m->mothurOut("Your file does not include the label " + *it);
 430                                 if (processedLabels.count(lastLabel) != 1) {
 431                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 432                                         needToRun = true;
 433                                 }else {
 434                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 435                                 }
 436                         }
 437
 438                         //run last label if you need to
 439                         if (needToRun == true)  {
 440                                 if (sabund != NULL) {   delete sabund;  }
 441                                 sabund = input->getSAbundVector(lastLabel);
 442
 443                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 444                                 outputFileHandle << sabund->getLabel();
 445                                 for(int i=0;i<sumCalculators.size();i++){
 446                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 447
 448                                         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;  }
 449
 450                                         outputFileHandle << '\t';
 451                                         sumCalculators[i]->print(outputFileHandle);
 452                                 }
 453                                 outputFileHandle << endl;
 454                                 numLines++;
 455                                 delete sabund;
 456                         }
 457
 458                         outputFileHandle.close();
 459
 460                         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;  }
 461
 462
 463                         delete input;
 464                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 465                 }
 466
 467                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 468
 469                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 470                 if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 471
 472                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 473
 474                 m->mothurOutEndLine();
 475                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 476                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 477                 m->mothurOutEndLine();
 478
 479                 return 0;
 480         }
 481         catch(exception& e) {
 482                 m->errorOut(e, "SummaryCommand", "execute");
 483                 exit(1);
 484         }
 485 }
 486 //**********************************************************************************************************************
 487 vector<string> SummaryCommand::parseSharedFile(string filename) {
 488         try {
 489                 vector<string> filenames;
 490
 491                 map<string, ofstream*> filehandles;
 492                 map<string, ofstream*>::iterator it3;
 493
 494                 input = new InputData(filename, "sharedfile");
 495                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 496
 497                 string sharedFileRoot = m->getRootName(filename);
 498
 499                 //clears file before we start to write to it below
 500                 for (int i=0; i<lookup.size(); i++) {
 501                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 502                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 503                 }
 504
 505                 ofstream* temp;
 506                 for (int i=0; i<lookup.size(); i++) {
 507                         temp = new ofstream;
 508                         filehandles[lookup[i]->getGroup()] = temp;
 509                         groups.push_back(lookup[i]->getGroup());
 510                 }
 511
 512                 while(lookup[0] != NULL) {
 513
 514                         for (int i = 0; i < lookup.size(); i++) {
 515                                 RAbundVector rav = lookup[i]->getRAbundVector();
 516                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 517                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 518                                 (*(filehandles[lookup[i]->getGroup()])).close();
 519                         }
 520
 521                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 522                         lookup = input->getSharedRAbundVectors();
 523                 }
 524
 525                 //free memory
 526                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 527                         delete it3->second;
 528                 }
 529
 530                 delete input;
 531
 532                 return filenames;
 533         }
 534         catch(exception& e) {
 535                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 536                 exit(1);
 537         }
 538 }
 539 //**********************************************************************************************************************
 540 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
 541         try {
 542
 543                 ofstream out;
 544                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
 545
 546                 //open combined file
 547                 m->openOutputFile(combineFileName, out);
 548
 549                 //open each groups summary file
 550                 string newLabel = "";
 551                 map<string, vector<string> > files;
 552                 for (int i=0; i<outputNames.size(); i++) {
 553                         vector<string> thisFilesLines;
 554
 555                         ifstream temp;
 556                         m->openInputFile(outputNames[i], temp);
 557
 558                         //read through first line - labels
 559                         string tempLabel;
 560                         if (i == 0) { //we want to save the labels to output below
 561                                 for (int j = 0; j < numCols+1; j++) {
 562                                         temp >> tempLabel;
 563
 564                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 565                                         }else{  newLabel += tempLabel + '\t';   }
 566                                 }
 567                         }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
 568
 569                         m->gobble(temp);
 570
 571                         //for each label
 572                         for (int k = 0; k < numLines; k++) {
 573
 574                                 string thisLine = "";
 575                                 string tempLabel;
 576
 577                                 for (int j = 0; j < numCols+1; j++) {
 578                                         temp >> tempLabel;
 579
 580                                         //save for later
 581                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 582                                         else{  thisLine += tempLabel + "\t";    }
 583                                 }
 584
 585                                 thisLine += "\n";
 586
 587                                 thisFilesLines.push_back(thisLine);
 588
 589                                 m->gobble(temp);
 590                         }
 591
 592                         files[outputNames[i]] = thisFilesLines;
 593
 594                         temp.close();
 595                         remove(outputNames[i].c_str());
 596                 }
 597
 598                 //output label line to new file
 599                 out << newLabel << endl;
 600
 601                 //for each label
 602                 for (int k = 0; k < numLines; k++) {
 603
 604                         //grab summary data for each group
 605                         for (int i=0; i<outputNames.size(); i++) {
 606                                 out << files[outputNames[i]][k];
 607                         }
 608                 }
 609
 610                 outputNames.clear();
 611
 612                 out.close();
 613
 614                 //return combine file name
 615                 return combineFileName;
 616
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 620                 exit(1);
 621         }
 622 }
 623 //**********************************************************************************************************************