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 #include "subsample.h"
  37
  38 //**********************************************************************************************************************
  39 vector<string> SummaryCommand::setParameters(){
  40         try {
  41                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  42                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  43                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  44                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  45         CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
  46         CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  47                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  48                 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-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);
  49                 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
  50                 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
  51                 CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
  52                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  53                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  54
  55                 vector<string> myArray;
  56                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "SummaryCommand", "setParameters");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 string SummaryCommand::getHelpString(){
  66         try {
  67                 string helpString = "";
  68                 ValidCalculators validCalculator;
  69                 helpString += "The summary.single command parameters are list, sabund, rabund, shared, subsample, iters, label, calc, abund and groupmode.  list, sabund, rabund or shared is required unless you have a valid current file.\n";
  70                 helpString += "The summary.single command should be in the following format: \n";
  71                 helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
  72                 helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
  73                 helpString += validCalculator.printCalc("summary");
  74         helpString += "The subsample parameter allows you to enter the size of the sample or you can set subsample=T and mothur will use the size of your smallest group in the case of a shared file. With a list, sabund or rabund file you must provide a subsample size.\n";
  75         helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
  76                 helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
  77                 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";
  78                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  79                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
  80                 return helpString;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "SummaryCommand", "getHelpString");
  84                 exit(1);
  85         }
  86 }
  87
  88 //**********************************************************************************************************************
  89 SummaryCommand::SummaryCommand(){
  90         try {
  91                 abort = true; calledHelp = true;
  92                 setParameters();
  93                 vector<string> tempOutNames;
  94                 outputTypes["summary"] = tempOutNames;
  95         }
  96         catch(exception& e) {
  97                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
  98                 exit(1);
  99         }
 100 }
 101 //**********************************************************************************************************************
 102
 103 SummaryCommand::SummaryCommand(string option)  {
 104         try {
 105                 abort = false; calledHelp = false;
 106                 allLines = 1;
 107
 108                 //allow user to run help
 109                 if(option == "help") {  help();  abort = true; calledHelp = true; }
 110                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 111
 112                 else {
 113                         vector<string> myArray = setParameters();
 114
 115                         OptionParser parser(option);
 116                         map<string,string> parameters = parser.getParameters();
 117                         map<string,string>::iterator it;
 118
 119                         ValidParameters validParameter;
 120
 121                         //check to make sure all parameters are valid for command
 122                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 123                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 124                         }
 125
 126                         //initialize outputTypes
 127                         vector<string> tempOutNames;
 128                         outputTypes["summary"] = tempOutNames;
 129
 130                         //if the user changes the input directory command factory will send this info to us in the output parameter
 131                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 132                         if (inputDir == "not found"){   inputDir = "";          }
 133                         else {
 134                                 string path;
 135                                 it = parameters.find("shared");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 141                                 }
 142
 143                                 it = parameters.find("rabund");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 149                                 }
 150
 151                                 it = parameters.find("sabund");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 157                                 }
 158
 159                                 it = parameters.find("list");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 165                                 }
 166                         }
 167
 168                         //check for required parameters
 169                         listfile = validParameter.validFile(parameters, "list", true);
 170                         if (listfile == "not open") { listfile = ""; abort = true; }
 171                         else if (listfile == "not found") { listfile = ""; }
 172                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 173
 174                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 175                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 176                         else if (sabundfile == "not found") { sabundfile = ""; }
 177                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 178
 179                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 180                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 181                         else if (rabundfile == "not found") { rabundfile = ""; }
 182                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 183
 184                         sharedfile = validParameter.validFile(parameters, "shared", true);
 185                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 186                         else if (sharedfile == "not found") { sharedfile = ""; }
 187                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 188
 189                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 190                                 //is there are current file available for any of these?
 191                                 //give priority to shared, then list, then rabund, then sabund
 192                                 //if there is a current shared file, use it
 193                                 sharedfile = m->getSharedFile();
 194                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 195                                 else {
 196                                         listfile = m->getListFile();
 197                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 198                                         else {
 199                                                 rabundfile = m->getRabundFile();
 200                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 201                                                 else {
 202                                                         sabundfile = m->getSabundFile();
 203                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 204                                                         else {
 205                                                                 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();
 206                                                                 abort = true;
 207                                                         }
 208                                                 }
 209                                         }
 210                                 }
 211                         }
 212
 213                         //if the user changes the output directory command factory will send this info to us in the output parameter
 214                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 215
 216                         //check for optional parameter and set defaults
 217                         // ...at some point should added some additional type checking...
 218                         label = validParameter.validFile(parameters, "label", false);
 219                         if (label == "not found") { label = ""; }
 220                         else {
 221                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 222                                 else { allLines = 1;  }
 223                         }
 224
 225                         calc = validParameter.validFile(parameters, "calc", false);
 226                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 227                         else {
 228                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 229                         }
 230                         m->splitAtDash(calc, Estimators);
 231                         if (m->inUsersGroups("citation", Estimators)) {
 232                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 233                                 //remove citation from list of calcs
 234                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 235                         }
 236
 237                         string temp;
 238                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 239                         m->mothurConvert(temp, abund);
 240
 241                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 242                         m->mothurConvert(temp, size);
 243
 244                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 245                         groupMode = m->isTrue(temp);
 246
 247             temp = validParameter.validFile(parameters, "iters", false);                        if (temp == "not found") { temp = "1000"; }
 248                         m->mothurConvert(temp, iters);
 249
 250             temp = validParameter.validFile(parameters, "subsample", false);            if (temp == "not found") { temp = "F"; }
 251                         if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
 252             else {
 253                 if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; }  //we will set it to smallest group later
 254                 else { subsample = false; subsampleSize = -1; }
 255             }
 256
 257             if (subsample == false) { iters = 1; }
 258             else {
 259                 //if you did not set a samplesize and are not using a sharedfile
 260                 if ((subsampleSize == -1) && (format != "sharedfile"))  { m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size.  You can do this by setting subsample=yourSampleSize.\n");  abort=true; }
 261             }
 262
 263                 }
 264         }
 265         catch(exception& e) {
 266                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 267                 exit(1);
 268         }
 269 }
 270 //**********************************************************************************************************************
 271
 272 int SummaryCommand::execute(){
 273         try {
 274
 275                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 276
 277                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 278                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 279
 280                 if (m->control_pressed) { return 0; }
 281
 282                 int numLines = 0;
 283                 int numCols = 0;
 284                 map<string, string> groupIndex;
 285
 286                 for (int p = 0; p < inputFileNames.size(); p++) {
 287
 288                         numLines = 0;
 289                         numCols = 0;
 290
 291                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
 292             string fileNameAve = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "ave";
 293             string fileNameSTD = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "std";
 294                         outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
 295
 296
 297
 298                         if (inputFileNames.size() > 1) {
 299                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 300                 groupIndex[fileNameRoot] = groups[p];
 301                         }
 302
 303                         sumCalculators.clear();
 304
 305                         ValidCalculators validCalculator;
 306
 307                         for (int i=0; i<Estimators.size(); i++) {
 308                                 if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
 309                                         if(Estimators[i] == "sobs"){
 310                                                 sumCalculators.push_back(new Sobs());
 311                                         }else if(Estimators[i] == "chao"){
 312                                                 sumCalculators.push_back(new Chao1());
 313                                         }else if(Estimators[i] == "coverage"){
 314                                                 sumCalculators.push_back(new Coverage());
 315                                         }else if(Estimators[i] == "geometric"){
 316                                                 sumCalculators.push_back(new Geom());
 317                                         }else if(Estimators[i] == "logseries"){
 318                                                 sumCalculators.push_back(new LogSD());
 319                                         }else if(Estimators[i] == "qstat"){
 320                                                 sumCalculators.push_back(new QStat());
 321                                         }else if(Estimators[i] == "bergerparker"){
 322                                                 sumCalculators.push_back(new BergerParker());
 323                                         }else if(Estimators[i] == "bstick"){
 324                                                 sumCalculators.push_back(new BStick());
 325                                         }else if(Estimators[i] == "ace"){
 326                                                 if(abund < 5)
 327                                                         abund = 10;
 328                                                 sumCalculators.push_back(new Ace(abund));
 329                                         }else if(Estimators[i] == "jack"){
 330                                                 sumCalculators.push_back(new Jackknife());
 331                                         }else if(Estimators[i] == "shannon"){
 332                                                 sumCalculators.push_back(new Shannon());
 333                                         }else if(Estimators[i] == "shannoneven"){
 334                                                 sumCalculators.push_back(new ShannonEven());
 335                                         }else if(Estimators[i] == "npshannon"){
 336                                                 sumCalculators.push_back(new NPShannon());
 337                                         }else if(Estimators[i] == "heip"){
 338                                                 sumCalculators.push_back(new Heip());
 339                                         }else if(Estimators[i] == "smithwilson"){
 340                                                 sumCalculators.push_back(new SmithWilson());
 341                                         }else if(Estimators[i] == "simpson"){
 342                                                 sumCalculators.push_back(new Simpson());
 343                                         }else if(Estimators[i] == "simpsoneven"){
 344                                                 sumCalculators.push_back(new SimpsonEven());
 345                                         }else if(Estimators[i] == "invsimpson"){
 346                                                 sumCalculators.push_back(new InvSimpson());
 347                                         }else if(Estimators[i] == "bootstrap"){
 348                                                 sumCalculators.push_back(new Bootstrap());
 349                                         }else if (Estimators[i] == "nseqs") {
 350                                                 sumCalculators.push_back(new NSeqs());
 351                                         }else if (Estimators[i] == "goodscoverage") {
 352                                                 sumCalculators.push_back(new GoodsCoverage());
 353                                         }else if (Estimators[i] == "efron") {
 354                                                 sumCalculators.push_back(new Efron(size));
 355                                         }else if (Estimators[i] == "boneh") {
 356                                                 sumCalculators.push_back(new Boneh(size));
 357                                         }else if (Estimators[i] == "solow") {
 358                                                 sumCalculators.push_back(new Solow(size));
 359                                         }else if (Estimators[i] == "shen") {
 360                                                 sumCalculators.push_back(new Shen(size, abund));
 361                                         }
 362                                 }
 363                         }
 364
 365                         //if the users entered no valid calculators don't execute command
 366                         if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0; }
 367
 368                         ofstream outputFileHandle;
 369                         m->openOutputFile(fileNameRoot, outputFileHandle);
 370                         outputFileHandle << "label";
 371
 372             ofstream outAve, outSTD;
 373             if (subsample) {
 374                 m->openOutputFile(fileNameAve, outAve);
 375                 m->openOutputFile(fileNameSTD, outSTD);
 376                 outputNames.push_back(fileNameAve); outputTypes["ave"].push_back(fileNameAve);
 377                 outputNames.push_back(fileNameSTD); outputTypes["std"].push_back(fileNameSTD);
 378                 outAve << "label"; outSTD << "label";
 379                 outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
 380                 outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
 381                 if (inputFileNames.size() > 1) {
 382                     groupIndex[fileNameAve] = groups[p];
 383                     groupIndex[fileNameSTD] = groups[p];
 384                 }
 385             }
 386
 387                         input = new InputData(inputFileNames[p], format);
 388                         sabund = input->getSAbundVector();
 389                         string lastLabel = sabund->getLabel();
 390
 391                         for(int i=0;i<sumCalculators.size();i++){
 392                                 if(sumCalculators[i]->getCols() == 1){
 393                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 394                     if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); outSTD << '\t' << sumCalculators[i]->getName(); }
 395                                         numCols++;
 396                                 }
 397                                 else{
 398                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 399                     if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; outSTD << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
 400                                         numCols += 3;
 401                                 }
 402                         }
 403                         outputFileHandle << endl;
 404             if (subsample) { outSTD << endl; outAve << endl; }
 405
 406                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 407                         set<string> processedLabels;
 408                         set<string> userLabels = labels;
 409
 410
 411
 412                         if (m->control_pressed) {  outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 413
 414                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 415
 416                                 if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 417
 418                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 419
 420                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 421                                         processedLabels.insert(sabund->getLabel());
 422                                         userLabels.erase(sabund->getLabel());
 423
 424                     process(sabund, outputFileHandle, outAve, outSTD);
 425
 426                     if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 427                                         numLines++;
 428                                 }
 429
 430                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 431                                         string saveLabel = sabund->getLabel();
 432
 433                                         delete sabund;
 434                                         sabund = input->getSAbundVector(lastLabel);
 435
 436                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 437                                         processedLabels.insert(sabund->getLabel());
 438                                         userLabels.erase(sabund->getLabel());
 439
 440                     process(sabund, outputFileHandle, outAve, outSTD);
 441
 442                     if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 443                                         numLines++;
 444
 445                                         //restore real lastlabel to save below
 446                                         sabund->setLabel(saveLabel);
 447                                 }
 448
 449                                 lastLabel = sabund->getLabel();
 450
 451                                 delete sabund;
 452                                 sabund = input->getSAbundVector();
 453                         }
 454
 455                         if (m->control_pressed) {  outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 456
 457                         //output error messages about any remaining user labels
 458                         set<string>::iterator it;
 459                         bool needToRun = false;
 460                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 461                                 m->mothurOut("Your file does not include the label " + *it);
 462                                 if (processedLabels.count(lastLabel) != 1) {
 463                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 464                                         needToRun = true;
 465                                 }else {
 466                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 467                                 }
 468                         }
 469
 470                         //run last label if you need to
 471                         if (needToRun == true)  {
 472                                 if (sabund != NULL) {   delete sabund;  }
 473                                 sabund = input->getSAbundVector(lastLabel);
 474
 475                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 476                 process(sabund, outputFileHandle, outAve, outSTD);
 477
 478                 if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 479                                 numLines++;
 480                                 delete sabund;
 481                         }
 482
 483                         outputFileHandle.close();
 484             if (subsample) { outAve.close(); outSTD.close(); }
 485
 486                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 487
 488
 489                         delete input;
 490                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 491                 }
 492
 493                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  return 0;  }
 494
 495                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 496                 if ((sharedfile != "") && (groupMode)) {   vector<string> comboNames = createGroupSummaryFile(numLines, numCols, outputNames, groupIndex);  for (int i = 0; i < comboNames.size(); i++) { outputNames.push_back(comboNames[i]); } }
 497
 498                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  return 0;  }
 499
 500                 m->mothurOutEndLine();
 501                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 502                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 503                 m->mothurOutEndLine();
 504
 505                 return 0;
 506         }
 507         catch(exception& e) {
 508                 m->errorOut(e, "SummaryCommand", "execute");
 509                 exit(1);
 510         }
 511 }
 512 //**********************************************************************************************************************
 513 int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve, ofstream& outStd) {
 514     try {
 515
 516         //calculator -> data -> values
 517         vector< vector< vector<double> > >  results; results.resize(sumCalculators.size());
 518
 519         outputFileHandle << sabund->getLabel();
 520
 521         SubSample sample;
 522         for (int thisIter = 0; thisIter < iters+1; thisIter++) {
 523
 524             SAbundVector* thisIterSabund = sabund;
 525
 526             //we want the summary results for the whole dataset, then the subsampling
 527             if ((thisIter > 0) && subsample) { //subsample sabund and run it
 528                 //copy sabund since getSample destroys it
 529                 RAbundVector rabund = sabund->getRAbundVector();
 530                 SAbundVector* newSabund = new SAbundVector();
 531                 *newSabund = rabund.getSAbundVector();
 532
 533                 sample.getSample(newSabund, subsampleSize);
 534                 thisIterSabund = newSabund;
 535             }
 536
 537             for(int i=0;i<sumCalculators.size();i++){
 538                 vector<double> data = sumCalculators[i]->getValues(thisIterSabund);
 539
 540                 if (m->control_pressed) {  return 0;  }
 541
 542                 if (thisIter == 0) {
 543                     outputFileHandle << '\t';
 544                     sumCalculators[i]->print(outputFileHandle);
 545                 }else {
 546                     //some of the calc have hci and lci need to make room for that
 547                     if (results[i].size() == 0) {  results[i].resize(data.size());  }
 548                     //save results for ave and std.
 549                     for (int j = 0; j < data.size(); j++) {
 550                         if (m->control_pressed) {  return 0;  }
 551                         results[i][j].push_back(data[j]);
 552                     }
 553                 }
 554             }
 555
 556             //cleanup memory
 557             if ((thisIter > 0) && subsample) { delete thisIterSabund; }
 558         }
 559         outputFileHandle << endl;
 560
 561         if (subsample) {
 562             outAve << sabund->getLabel() << '\t'; outStd << sabund->getLabel() << '\t';
 563             //find ave and std for this label and output
 564             //will need to modify the createGroupSummary to combine results and not mess with the .summary file.
 565
 566             //calcs -> values
 567             vector< vector<double> >  calcAverages; calcAverages.resize(sumCalculators.size());
 568             for (int i = 0; i < calcAverages.size(); i++) {  calcAverages[i].resize(results[i].size(), 0);  }
 569
 570             for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
 571                 for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
 572                     for (int j = 0; j < calcAverages[i].size(); j++) {
 573                         calcAverages[i][j] += results[i][j][thisIter];
 574                     }
 575                 }
 576             }
 577
 578             for (int i = 0; i < calcAverages.size(); i++) {  //finds average.
 579                 for (int j = 0; j < calcAverages[i].size(); j++) {
 580                     calcAverages[i][j] /= (float) iters;
 581                     outAve << calcAverages[i][j] << '\t';
 582                 }
 583             }
 584
 585             //find standard deviation
 586             vector< vector<double>  > stdDev; stdDev.resize(sumCalculators.size());
 587             for (int i = 0; i < stdDev.size(); i++) {  stdDev[i].resize(results[i].size(), 0);  }
 588
 589             for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
 590                 for (int i = 0; i < stdDev.size(); i++) {
 591                     for (int j = 0; j < stdDev[i].size(); j++) {
 592                         stdDev[i][j] += ((results[i][j][thisIter] - calcAverages[i][j]) * (results[i][j][thisIter] - calcAverages[i][j]));
 593                     }
 594                 }
 595             }
 596
 597             for (int i = 0; i < stdDev.size(); i++) {  //finds average.
 598                 for (int j = 0; j < stdDev[i].size(); j++) {
 599                     stdDev[i][j] /= (float) iters;
 600                     stdDev[i][j] = sqrt(stdDev[i][j]);
 601                     outStd << stdDev[i][j] << '\t';
 602                 }
 603             }
 604             outAve << endl;  outStd << endl;
 605         }
 606
 607         return 0;
 608     }
 609     catch(exception& e) {
 610         m->errorOut(e, "SummaryCommand", "process");
 611         exit(1);
 612     }
 613 }
 614 //**********************************************************************************************************************
 615 vector<string> SummaryCommand::parseSharedFile(string filename) {
 616         try {
 617                 vector<string> filenames;
 618
 619                 map<string, ofstream*> filehandles;
 620                 map<string, ofstream*>::iterator it3;
 621
 622                 input = new InputData(filename, "sharedfile");
 623                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 624
 625                 string sharedFileRoot = m->getRootName(filename);
 626
 627         /******************************************************/
 628         if (subsample) {
 629             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
 630                 subsampleSize = lookup[0]->getNumSeqs();
 631                 for (int i = 1; i < lookup.size(); i++) {
 632                     int thisSize = lookup[i]->getNumSeqs();
 633
 634                     if (thisSize < subsampleSize) {     subsampleSize = thisSize;       }
 635                 }
 636             }else {
 637                 m->clearGroups();
 638                 vector<string> Groups;
 639                 vector<SharedRAbundVector*> temp;
 640                 for (int i = 0; i < lookup.size(); i++) {
 641                     if (lookup[i]->getNumSeqs() < subsampleSize) {
 642                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 643                         delete lookup[i];
 644                     }else {
 645                         Groups.push_back(lookup[i]->getGroup());
 646                         temp.push_back(lookup[i]);
 647                     }
 648                 }
 649                 lookup = temp;
 650                 m->setGroups(Groups);
 651             }
 652
 653             if (lookup.size() < 1) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return filenames; }
 654         }
 655
 656
 657                 /******************************************************/
 658
 659         //clears file before we start to write to it below
 660                 for (int i=0; i<lookup.size(); i++) {
 661                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 662                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 663                 }
 664
 665                 ofstream* temp;
 666                 for (int i=0; i<lookup.size(); i++) {
 667                         temp = new ofstream;
 668                         filehandles[lookup[i]->getGroup()] = temp;
 669                         groups.push_back(lookup[i]->getGroup());
 670                 }
 671
 672                 while(lookup[0] != NULL) {
 673
 674                         for (int i = 0; i < lookup.size(); i++) {
 675                                 RAbundVector rav = lookup[i]->getRAbundVector();
 676                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 677                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 678                                 (*(filehandles[lookup[i]->getGroup()])).close();
 679                         }
 680
 681                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 682                         lookup = input->getSharedRAbundVectors();
 683                 }
 684
 685                 //free memory
 686                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 687                         delete it3->second;
 688                 }
 689
 690                 delete input;
 691
 692                 return filenames;
 693         }
 694         catch(exception& e) {
 695                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 696                 exit(1);
 697         }
 698 }
 699 //**********************************************************************************************************************
 700 vector<string> SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames, map<string, string> groupIndex) {
 701         try {
 702
 703                 //open each groups summary file
 704         vector<string> newComboNames;
 705                 string newLabel = "";
 706                 map<string, map<string, vector<string> > > files;
 707                 for (int i=0; i<outputNames.size(); i++) {
 708             string extension = m->getExtension(outputNames[i]);
 709             string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
 710                         m->mothurRemove(combineFileName); //remove old file
 711
 712                         vector<string> thisFilesLines;
 713
 714                         ifstream temp;
 715                         m->openInputFile(outputNames[i], temp);
 716
 717                         //read through first line - labels
 718                         string tempLabel;
 719                         if (i == 0) { //we want to save the labels to output below
 720                                 for (int j = 0; j < numCols+1; j++) {
 721                                         temp >> tempLabel;
 722
 723                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 724                                         }else{  newLabel += tempLabel + '\t';   }
 725                                 }
 726                         }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
 727
 728                         m->gobble(temp);
 729
 730                         //for each label
 731                         for (int k = 0; k < numLines; k++) {
 732
 733                                 string thisLine = "";
 734                                 string tempLabel;
 735
 736                                 for (int j = 0; j < numCols+1; j++) {
 737                                         temp >> tempLabel;
 738
 739                                         //save for later
 740                                         if (j == 1) { thisLine += groupIndex[outputNames[i]] + "\t" + tempLabel + "\t"; }
 741                                         else{  thisLine += tempLabel + "\t";    }
 742                                 }
 743
 744                                 thisLine += "\n";
 745
 746                                 thisFilesLines.push_back(thisLine);
 747
 748                                 m->gobble(temp);
 749                         }
 750
 751             map<string, map<string, vector<string> > >::iterator itFiles = files.find(extension);
 752             if (itFiles != files.end()) { //add new files info to existing type
 753                 files[extension][outputNames[i]] = thisFilesLines;
 754             }else {
 755                 map<string, vector<string> > thisFile;
 756                 thisFile[outputNames[i]] = thisFilesLines;
 757                 files[extension] = thisFile;
 758             }
 759
 760                         temp.close();
 761                         m->mothurRemove(outputNames[i]);
 762                 }
 763
 764
 765         for (map<string, map<string, vector<string> > >::iterator itFiles = files.begin(); itFiles != files.end(); itFiles++) {
 766
 767             if (m->control_pressed) { break; }
 768
 769             string extension = itFiles->first;
 770             map<string, vector<string> > thisType = itFiles->second;
 771             string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
 772             newComboNames.push_back(combineFileName);
 773             //open combined file
 774             ofstream out;
 775             m->openOutputFile(combineFileName, out);
 776
 777             //output label line to new file
 778             out << newLabel << endl;
 779
 780             //for each label
 781             for (int k = 0; k < numLines; k++) {
 782
 783                 //grab summary data for each group
 784                 for (map<string, vector<string> >::iterator itType = thisType.begin(); itType != thisType.end(); itType++) {
 785                     out << (itType->second)[k];
 786                 }
 787             }
 788
 789             outputNames.clear();
 790
 791             out.close();
 792         }
 793
 794                 //return combine file name
 795                 return newComboNames;
 796
 797         }
 798         catch(exception& e) {
 799                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 800                 exit(1);
 801         }
 802 }
 803 //**********************************************************************************************************************