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 "npshannon.h"
  18 #include "shannon.h"
  19 #include "jackknife.h"
  20 #include "geom.h"
  21 #include "logsd.h"
  22 #include "qstat.h"
  23 #include "bergerparker.h"
  24 #include "bstick.h"
  25 #include "goodscoverage.h"
  26 #include "coverage.h"
  27 #include "efron.h"
  28 #include "boneh.h"
  29 #include "solow.h"
  30 #include "shen.h"
  31
  32 //**********************************************************************************************************************
  33
  34 SummaryCommand::SummaryCommand(string option)  {
  35         try {
  36                 globaldata = GlobalData::getInstance();
  37                 abort = false;
  38                 allLines = 1;
  39                 labels.clear();
  40                 Estimators.clear();
  41
  42                 //allow user to run help
  43                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
  44
  45                 else {
  46                         //valid paramters for this command
  47                         string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
  48                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  49
  50                         OptionParser parser(option);
  51                         map<string,string> parameters = parser.getParameters();
  52
  53                         ValidParameters validParameter;
  54
  55                         //check to make sure all parameters are valid for command
  56                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  57                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  58                         }
  59
  60                         //make sure the user has already run the read.otu command
  61                         if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); m->mothurOutEndLine(); abort = true; }
  62
  63                         //if the user changes the output directory command factory will send this info to us in the output parameter
  64                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  65                                 outputDir = "";
  66                                 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  67                         }
  68
  69                         //check for optional parameter and set defaults
  70                         // ...at some point should added some additional type checking...
  71                         label = validParameter.validFile(parameters, "label", false);
  72                         if (label == "not found") { label = ""; }
  73                         else {
  74                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  75                                 else { allLines = 1;  }
  76                         }
  77
  78                         //if the user has not specified any labels use the ones from read.otu
  79                         if(label == "") {
  80                                 allLines = globaldata->allLines;
  81                                 labels = globaldata->labels;
  82                         }
  83
  84                         calc = validParameter.validFile(parameters, "calc", false);
  85                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
  86                         else {
  87                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
  88                         }
  89                         splitAtDash(calc, Estimators);
  90
  91                         string temp;
  92                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
  93                         convert(temp, abund);
  94
  95                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
  96                         convert(temp, size);
  97
  98                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "F"; }
  99                         groupMode = isTrue(temp);
 100
 101
 102                 }
 103         }
 104         catch(exception& e) {
 105                 m->errorOut(e, "SummaryCommand", "SummaryCommand");
 106                 exit(1);
 107         }
 108 }
 109 //**********************************************************************************************************************
 110
 111 void SummaryCommand::help(){
 112         try {
 113                 m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 114                 m->mothurOut("The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
 115                 m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode.  No parameters are required.\n");
 116                 m->mothurOut("The summary.single command should be in the following format: \n");
 117                 m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
 118                 m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
 119                 validCalculator->printCalc("summary", cout);
 120                 m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
 121                 m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=False).\n");
 122                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 123                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 124         }
 125         catch(exception& e) {
 126                 m->errorOut(e, "SummaryCommand", "help");
 127                 exit(1);
 128         }
 129 }
 130
 131 //**********************************************************************************************************************
 132
 133 SummaryCommand::~SummaryCommand(){}
 134
 135 //**********************************************************************************************************************
 136
 137 int SummaryCommand::execute(){
 138         try {
 139
 140                 if (abort == true) { return 0; }
 141
 142                 vector<string> outputNames;
 143
 144                 string hadShared = "";
 145                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 146                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 147
 148                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 149
 150                 int numLines = 0;
 151                 int numCols = 0;
 152
 153                 for (int p = 0; p < inputFileNames.size(); p++) {
 154
 155                         numLines = 0;
 156                         numCols = 0;
 157
 158                         string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary";
 159                         globaldata->inputFileName = inputFileNames[p];
 160                         outputNames.push_back(fileNameRoot);
 161
 162                         if (inputFileNames.size() > 1) {
 163                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 164                         }
 165
 166                         sumCalculators.clear();
 167
 168                         validCalculator = new ValidCalculators();
 169
 170                         for (int i=0; i<Estimators.size(); i++) {
 171                                 if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
 172                                         if(Estimators[i] == "sobs"){
 173                                                 sumCalculators.push_back(new Sobs());
 174                                         }else if(Estimators[i] == "chao"){
 175                                                 sumCalculators.push_back(new Chao1());
 176                                         }else if(Estimators[i] == "coverage"){
 177                                                 sumCalculators.push_back(new Coverage());
 178                                         }else if(Estimators[i] == "geometric"){
 179                                                 sumCalculators.push_back(new Geom());
 180                                         }else if(Estimators[i] == "logseries"){
 181                                                 sumCalculators.push_back(new LogSD());
 182                                         }else if(Estimators[i] == "qstat"){
 183                                                 sumCalculators.push_back(new QStat());
 184                                         }else if(Estimators[i] == "bergerparker"){
 185                                                 sumCalculators.push_back(new BergerParker());
 186                                         }else if(Estimators[i] == "bstick"){
 187                                                 sumCalculators.push_back(new BStick());
 188                                         }else if(Estimators[i] == "ace"){
 189                                                 if(abund < 5)
 190                                                         abund = 10;
 191                                                 sumCalculators.push_back(new Ace(abund));
 192                                         }else if(Estimators[i] == "jack"){
 193                                                 sumCalculators.push_back(new Jackknife());
 194                                         }else if(Estimators[i] == "shannon"){
 195                                                 sumCalculators.push_back(new Shannon());
 196                                         }else if(Estimators[i] == "npshannon"){
 197                                                 sumCalculators.push_back(new NPShannon());
 198                                         }else if(Estimators[i] == "simpson"){
 199                                                 sumCalculators.push_back(new Simpson());
 200                                         }else if(Estimators[i] == "bootstrap"){
 201                                                 sumCalculators.push_back(new Bootstrap());
 202                                         }else if (Estimators[i] == "nseqs") {
 203                                                 sumCalculators.push_back(new NSeqs());
 204                                         }else if (Estimators[i] == "goodscoverage") {
 205                                                 sumCalculators.push_back(new GoodsCoverage());
 206                                         }else if (Estimators[i] == "efron") {
 207                                                 sumCalculators.push_back(new Efron(size));
 208                                         }else if (Estimators[i] == "boneh") {
 209                                                 sumCalculators.push_back(new Boneh(size));
 210                                         }else if (Estimators[i] == "solow") {
 211                                                 sumCalculators.push_back(new Solow(size));
 212                                         }else if (Estimators[i] == "shen") {
 213                                                 sumCalculators.push_back(new Shen(size, abund));
 214                                         }
 215                                 }
 216                         }
 217
 218                         //if the users entered no valid calculators don't execute command
 219                         if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 220
 221                         ofstream outputFileHandle;
 222                         openOutputFile(fileNameRoot, outputFileHandle);
 223                         outputFileHandle << "label";
 224
 225                         read = new ReadOTUFile(globaldata->inputFileName);
 226                         read->read(&*globaldata);
 227
 228                         sabund = globaldata->sabund;
 229                         string lastLabel = sabund->getLabel();
 230                         input = globaldata->ginput;
 231
 232                         for(int i=0;i<sumCalculators.size();i++){
 233                                 if(sumCalculators[i]->getCols() == 1){
 234                                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 235                                         numCols++;
 236                                 }
 237                                 else{
 238                                         outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 239                                         numCols += 3;
 240                                 }
 241                         }
 242                         outputFileHandle << endl;
 243
 244                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 245                         set<string> processedLabels;
 246                         set<string> userLabels = labels;
 247
 248                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 249
 250                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 251
 252                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 253
 254                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 255
 256                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 257                                         processedLabels.insert(sabund->getLabel());
 258                                         userLabels.erase(sabund->getLabel());
 259
 260                                         outputFileHandle << sabund->getLabel();
 261                                         for(int i=0;i<sumCalculators.size();i++){
 262                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 263
 264                                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 265
 266                                                 outputFileHandle << '\t';
 267                                                 sumCalculators[i]->print(outputFileHandle);
 268                                         }
 269                                         outputFileHandle << endl;
 270                                         numLines++;
 271                                 }
 272
 273                                 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 274                                         string saveLabel = sabund->getLabel();
 275
 276                                         delete sabund;
 277                                         sabund = input->getSAbundVector(lastLabel);
 278
 279                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 280                                         processedLabels.insert(sabund->getLabel());
 281                                         userLabels.erase(sabund->getLabel());
 282
 283                                         outputFileHandle << sabund->getLabel();
 284                                         for(int i=0;i<sumCalculators.size();i++){
 285                                                 vector<double> data = sumCalculators[i]->getValues(sabund);
 286
 287                                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 288
 289                                                 outputFileHandle << '\t';
 290                                                 sumCalculators[i]->print(outputFileHandle);
 291                                         }
 292                                         outputFileHandle << endl;
 293                                         numLines++;
 294
 295                                         //restore real lastlabel to save below
 296                                         sabund->setLabel(saveLabel);
 297                                 }
 298
 299                                 lastLabel = sabund->getLabel();
 300
 301                                 delete sabund;
 302                                 sabund = input->getSAbundVector();
 303                         }
 304
 305                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 306
 307                         //output error messages about any remaining user labels
 308                         set<string>::iterator it;
 309                         bool needToRun = false;
 310                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 311                                 m->mothurOut("Your file does not include the label " + *it);
 312                                 if (processedLabels.count(lastLabel) != 1) {
 313                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 314                                         needToRun = true;
 315                                 }else {
 316                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 317                                 }
 318                         }
 319
 320                         //run last label if you need to
 321                         if (needToRun == true)  {
 322                                 if (sabund != NULL) {   delete sabund;  }
 323                                 sabund = input->getSAbundVector(lastLabel);
 324
 325                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 326                                 outputFileHandle << sabund->getLabel();
 327                                 for(int i=0;i<sumCalculators.size();i++){
 328                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 329
 330                                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 331
 332                                         outputFileHandle << '\t';
 333                                         sumCalculators[i]->print(outputFileHandle);
 334                                 }
 335                                 outputFileHandle << endl;
 336                                 numLines++;
 337                                 delete sabund;
 338                         }
 339
 340                         outputFileHandle.close();
 341
 342                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 343
 344
 345                         delete input;  globaldata->ginput = NULL;
 346                         delete read;
 347                         delete validCalculator;
 348                         globaldata->sabund = NULL;
 349                         for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 350                 }
 351
 352                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 353
 354                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 355
 356                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 357                 if ((hadShared != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 358
 359                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
 360
 361                 m->mothurOutEndLine();
 362                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 363                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 364                 m->mothurOutEndLine();
 365
 366                 return 0;
 367         }
 368         catch(exception& e) {
 369                 m->errorOut(e, "SummaryCommand", "execute");
 370                 exit(1);
 371         }
 372 }
 373 //**********************************************************************************************************************
 374 vector<string> SummaryCommand::parseSharedFile(string filename) {
 375         try {
 376                 vector<string> filenames;
 377
 378                 map<string, ofstream*> filehandles;
 379                 map<string, ofstream*>::iterator it3;
 380
 381
 382                 //read first line
 383                 read = new ReadOTUFile(filename);
 384                 read->read(&*globaldata);
 385
 386                 input = globaldata->ginput;
 387                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 388
 389                 string sharedFileRoot = getRootName(filename);
 390
 391                 //clears file before we start to write to it below
 392                 for (int i=0; i<lookup.size(); i++) {
 393                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 394                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 395                 }
 396
 397                 ofstream* temp;
 398                 for (int i=0; i<lookup.size(); i++) {
 399                         temp = new ofstream;
 400                         filehandles[lookup[i]->getGroup()] = temp;
 401                         groups.push_back(lookup[i]->getGroup());
 402                 }
 403
 404                 while(lookup[0] != NULL) {
 405
 406                         for (int i = 0; i < lookup.size(); i++) {
 407                                 RAbundVector rav = lookup[i]->getRAbundVector();
 408                                 openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 409                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 410                                 (*(filehandles[lookup[i]->getGroup()])).close();
 411                         }
 412
 413                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 414                         lookup = input->getSharedRAbundVectors();
 415                 }
 416
 417                 //free memory
 418                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 419                         delete it3->second;
 420                 }
 421                 delete read;
 422                 delete input;
 423                 globaldata->ginput = NULL;
 424
 425                 return filenames;
 426         }
 427         catch(exception& e) {
 428                 m->errorOut(e, "SummaryCommand", "parseSharedFile");
 429                 exit(1);
 430         }
 431 }
 432 //**********************************************************************************************************************
 433 string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string> outputNames) {
 434         try {
 435
 436                 ofstream out;
 437                 string combineFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "groups.summary";
 438
 439                 //open combined file
 440                 openOutputFile(combineFileName, out);
 441
 442                 //open each groups summary file
 443                 string newLabel = "";
 444                 ifstream* temp;
 445                 map<string, ifstream*> filehandles;
 446                 for (int i=0; i<outputNames.size(); i++) {
 447                         temp = new ifstream;
 448                         filehandles[outputNames[i]] = temp;
 449                         openInputFile(outputNames[i], *(temp));
 450
 451                         //read through first line - labels
 452                         string tempLabel;
 453                         if (i == 0) { //we want to save the labels to output below
 454                                 for (int j = 0; j < numCols+1; j++) {
 455                                         *(temp) >> tempLabel;
 456
 457                                         if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
 458                                         }else{  newLabel += tempLabel + '\t';   }
 459                                 }
 460                         }else{  for (int j = 0; j < numCols+1; j++) {  *(temp) >> tempLabel;  }  }
 461
 462                         gobble(*(temp));
 463                 }
 464
 465                 //output label line to new file
 466                 out << newLabel << endl;
 467
 468                 //for each label
 469                 for (int i = 0; i < numLines; i++) {
 470
 471                         //grab summary data for each group
 472                         for (int i=0; i<outputNames.size(); i++) {
 473                                 string tempLabel;
 474
 475                                 for (int j = 0; j < numCols+1; j++) {
 476                                         *(filehandles[outputNames[i]]) >> tempLabel;
 477
 478                                         //print to combined file
 479                                         if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t';    }
 480                                         else{  out << tempLabel << '\t';        }
 481                                 }
 482
 483                                 out << endl;
 484                                 gobble(*(filehandles[outputNames[i]]));
 485                         }
 486                 }
 487
 488                 //close each groups summary file
 489                 for (int i=0; i<outputNames.size(); i++) {  (*(filehandles[outputNames[i]])).close();  }
 490                 out.close();
 491
 492                 //return combine file name
 493                 return combineFileName;
 494
 495         }
 496         catch(exception& e) {
 497                 m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
 498                 exit(1);
 499         }
 500 }
 501 //**********************************************************************************************************************