bootstrapsharedcommand.cpp

   1 /*
   2  *  bootstrapsharedcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/16/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "bootstrapsharedcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24 vector<string> BootSharedCommand::setParameters(){
  25         try {
  26                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
  27                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  28                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  29                 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  30                 CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "BootSharedCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string BootSharedCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The bootstrap.shared command parameters are shared, groups, calc, iters and label. shared is required.\n";
  48                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  49                 helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n";
  50                 helpString += "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n";
  51                 helpString += "Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n";
  52                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  53                 helpString += "The default value for calc is jclass-thetayc. The default for iters is 1000.\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "BootSharedCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 BootSharedCommand::BootSharedCommand(){
  63         try {
  64                 abort = true; calledHelp = true;
  65                 setParameters();
  66                 vector<string> tempOutNames;
  67                 outputTypes["tree"] = tempOutNames;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 BootSharedCommand::BootSharedCommand(string option) {
  76         try {
  77                 abort = false; calledHelp = false;
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  82
  83                 else {
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88                         map<string,string>::iterator it;
  89
  90                         ValidParameters validParameter;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["tree"] = tempOutNames;
 100
 101                         //if the user changes the input directory command factory will send this info to us in the output parameter
 102                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 103                         if (inputDir == "not found"){   inputDir = "";          }
 104                         else {
 105                                 string path;
 106                                 it = parameters.find("shared");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 112                                 }
 113                         }
 114
 115                         sharedfile = validParameter.validFile(parameters, "shared", true);
 116                         if (sharedfile == "not found") {
 117                                 sharedfile = m->getSharedFile();
 118                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 119                                 else {  m->mothurOut("You have no current shared file and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 120                         }
 121                         else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 122                         else { m->setSharedFile(sharedfile); }
 123
 124                         //if the user changes the output directory command factory will send this info to us in the output parameter
 125                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 126                                 outputDir = "";
 127                                 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 128                         }
 129
 130                         //check for optional parameter and set defaults
 131                         // ...at some point should added some additional type checking...
 132                         label = validParameter.validFile(parameters, "label", false);
 133                         if (label == "not found") { label = ""; }
 134                         else {
 135                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 136                                 else { allLines = 1;  }
 137                         }
 138
 139                         groups = validParameter.validFile(parameters, "groups", false);
 140                         if (groups == "not found") { groups = ""; }
 141                         else {
 142                                 m->splitAtDash(groups, Groups);
 143                                 m->setGroups(Groups);
 144                         }
 145
 146                         calc = validParameter.validFile(parameters, "calc", false);
 147                         if (calc == "not found") { calc = "jclass-thetayc";  }
 148                         else {
 149                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 150                         }
 151                         m->splitAtDash(calc, Estimators);
 152                         if (m->inUsersGroups("citation", Estimators)) {
 153                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 154                                 //remove citation from list of calcs
 155                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 156                         }
 157
 158                         string temp;
 159                         temp = validParameter.validFile(parameters, "iters", false);  if (temp == "not found") { temp = "1000"; }
 160                         m->mothurConvert(temp, iters);
 161
 162                         if (abort == false) {
 163
 164                                 //used in tree constructor
 165                                 m->runParse = false;
 166
 167                                 validCalculator = new ValidCalculators();
 168
 169
 170                                 //NOTE: if you add a calc to this if statement you must add it to the setParameters function
 171                                 //or it will not be visible in the gui
 172                                 int i;
 173                                 for (i=0; i<Estimators.size(); i++) {
 174                                         if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
 175                                                 if (Estimators[i] == "jabund") {
 176                                                         treeCalculators.push_back(new JAbund());
 177                                                 }else if (Estimators[i] == "sorabund") {
 178                                                         treeCalculators.push_back(new SorAbund());
 179                                                 }else if (Estimators[i] == "jclass") {
 180                                                         treeCalculators.push_back(new Jclass());
 181                                                 }else if (Estimators[i] == "sorclass") {
 182                                                         treeCalculators.push_back(new SorClass());
 183                                                 }else if (Estimators[i] == "jest") {
 184                                                         treeCalculators.push_back(new Jest());
 185                                                 }else if (Estimators[i] == "sorest") {
 186                                                         treeCalculators.push_back(new SorEst());
 187                                                 }else if (Estimators[i] == "thetayc") {
 188                                                         treeCalculators.push_back(new ThetaYC());
 189                                                 }else if (Estimators[i] == "thetan") {
 190                                                         treeCalculators.push_back(new ThetaN());
 191                                                 }else if (Estimators[i] == "morisitahorn") {
 192                                                         treeCalculators.push_back(new MorHorn());
 193                                                 }else if (Estimators[i] == "braycurtis") {
 194                                                         treeCalculators.push_back(new BrayCurtis());
 195                                                 }
 196                                         }
 197                                 }
 198
 199                                 delete validCalculator;
 200
 201                                 ofstream* tempo;
 202                                 for (int i=0; i < treeCalculators.size(); i++) {
 203                                         tempo = new ofstream;
 204                                         out.push_back(tempo);
 205                                 }
 206
 207                                 //make a vector of tree* for each calculator
 208                                 trees.resize(treeCalculators.size());
 209                         }
 210                 }
 211
 212         }
 213         catch(exception& e) {
 214                 m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
 215                 exit(1);
 216         }
 217 }
 218 //**********************************************************************************************************************
 219 BootSharedCommand::~BootSharedCommand(){}
 220 //**********************************************************************************************************************
 221
 222 int BootSharedCommand::execute(){
 223         try {
 224
 225                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 226
 227                 m->mothurOut("bootstrap.shared command is no longer available."); m->mothurOutEndLine();
 228         /*
 229                 //read first line
 230                 input = new InputData(sharedfile, "sharedfile");
 231                 order = input->getSharedOrderVector();
 232                 string lastLabel = order->getLabel();
 233
 234                 //if the users entered no valid calculators don't execute command
 235                 if (treeCalculators.size() == 0) { return 0; }
 236
 237                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 238                 set<string> processedLabels;
 239                 set<string> userLabels = labels;
 240
 241                 //set users groups
 242                 util = new SharedUtil();
 243                 util->setGroups(m->Groups, m->namesOfGroups, "treegroup");
 244
 245                 numGroups = m->Groups.size();
 246
 247                 //clear globaldatas old tree names if any
 248                 globaldata->Treenames.clear();
 249
 250                 //fills globaldatas tree names
 251                 globaldata->Treenames = m->Groups;
 252
 253                 //create treemap class from groupmap for tree class to use
 254                 tmap = new TreeMap();
 255                 tmap->makeSim(globaldata->gGroupmap);
 256                 globaldata->gTreemap = tmap;
 257
 258                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 259                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear(); delete input;delete util; return 0;     }
 260
 261                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 262
 263                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 264                                 int error = process(order);
 265                                 if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear(); delete input;delete util; return 0;     }
 266
 267                                 processedLabels.insert(order->getLabel());
 268                                 userLabels.erase(order->getLabel());
 269                         }
 270
 271                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 272                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 273                                 string saveLabel = order->getLabel();
 274
 275                                 delete order;
 276                                 order = input->getSharedOrderVector(lastLabel);
 277                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 278                                 int error = process(order);
 279                                 if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear(); delete input;delete util; return 0;     }
 280
 281                                 processedLabels.insert(order->getLabel());
 282                                 userLabels.erase(order->getLabel());
 283
 284                                 //restore real lastlabel to save below
 285                                 order->setLabel(saveLabel);
 286                         }
 287
 288
 289                         lastLabel = order->getLabel();
 290
 291                         //get next line to process
 292                         delete order;
 293                         order = input->getSharedOrderVector();
 294                 }
 295
 296
 297                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear(); delete input; delete util;  return 0;   }
 298
 299                 //output error messages about any remaining user labels
 300                 set<string>::iterator it;
 301                 bool needToRun = false;
 302                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 303                         m->mothurOut("Your file does not include the label " + *it);
 304                         if (processedLabels.count(lastLabel) != 1) {
 305                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 306                                 needToRun = true;
 307                         }else {
 308                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 309                         }
 310                 }
 311
 312                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear(); delete input; delete util; return 0;    }
 313
 314                 //run last line if you need to
 315                 if (needToRun == true)  {
 316                                 if (order != NULL) {    delete order;   }
 317                                 order = input->getSharedOrderVector(lastLabel);
 318                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 319                                 int error = process(order);
 320                                 if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear(); delete input; delete util; return 0;    }
 321
 322                                 delete order;
 323
 324                 }
 325
 326                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } globaldata->Groups.clear();delete input; delete util; return 0;     }
 327
 328                 //reset groups parameter
 329                 globaldata->Groups.clear();
 330
 331                 //set first tree file as new current treefile
 332                 string currentTree = "";
 333                 itTypes = outputTypes.find("tree");
 334                 if (itTypes != outputTypes.end()) {
 335                         if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
 336                 }
 337
 338                 delete input;
 339                 delete util;
 340
 341                 m->mothurOutEndLine();
 342                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 343                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 344                 m->mothurOutEndLine();
 345 */
 346
 347                 return 0;
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "BootSharedCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354 //**********************************************************************************************************************
 355
 356 int BootSharedCommand::createTree(ostream* out, Tree* t){
 357         try {
 358                 /*
 359                 //do merges and create tree structure by setting parents and children
 360                 //there are numGroups - 1 merges to do
 361                 for (int i = 0; i < (numGroups - 1); i++) {
 362
 363                         if (m->control_pressed) {  return 1; }
 364
 365                         float largest = -1000.0;
 366                         int row, column;
 367                         //find largest value in sims matrix by searching lower triangle
 368                         for (int j = 1; j < simMatrix.size(); j++) {
 369                                 for (int k = 0; k < j; k++) {
 370                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 371                                 }
 372                         }
 373
 374                         //set non-leaf node info and update leaves to know their parents
 375                         //non-leaf
 376                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 377
 378                         //parents
 379                         t->tree[index[row]].setParent(numGroups + i);
 380                         t->tree[index[column]].setParent(numGroups + i);
 381
 382                         //blength = distance / 2;
 383                         float blength = ((1.0 - largest) / 2);
 384
 385                         //branchlengths
 386                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 387                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 388
 389                         //set your length to leaves to your childs length plus branchlength
 390                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 391
 392
 393                         //update index
 394                         index[row] = numGroups+i;
 395                         index[column] = numGroups+i;
 396
 397                         //zero out highest value that caused the merge.
 398                         simMatrix[row][column] = -1000.0;
 399                         simMatrix[column][row] = -1000.0;
 400
 401                         //merge values in simsMatrix
 402                         for (int n = 0; n < simMatrix.size(); n++)      {
 403                                 //row becomes merge of 2 groups
 404                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 405                                 simMatrix[n][row] = simMatrix[row][n];
 406                                 //delete column
 407                                 simMatrix[column][n] = -1000.0;
 408                                 simMatrix[n][column] = -1000.0;
 409                         }
 410                 }
 411
 412                 //adjust tree to make sure root to tip length is .5
 413                 int root = t->findRoot();
 414                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 415
 416                 //assemble tree
 417                 t->assembleTree();
 418
 419                 if (m->control_pressed) { return 1; }
 420
 421                 //print newick file
 422                 t->print(*out);*/
 423
 424                 return 0;
 425
 426         }
 427         catch(exception& e) {
 428                 m->errorOut(e, "BootSharedCommand", "createTree");
 429                 exit(1);
 430         }
 431 }
 432 /***********************************************************/
 433 void BootSharedCommand::printSims() {
 434         try {
 435                 m->mothurOut("simsMatrix"); m->mothurOutEndLine();
 436                 for (int k = 0; k < simMatrix.size(); k++)      {
 437                         for (int n = 0; n < simMatrix.size(); n++)      {
 438                                 m->mothurOut(toString(simMatrix[k][n]));  m->mothurOut("\t");
 439                         }
 440                         m->mothurOutEndLine();
 441                 }
 442
 443         }
 444         catch(exception& e) {
 445                 m->errorOut(e, "BootSharedCommand", "printSims");
 446                 exit(1);
 447         }
 448 }
 449 /***********************************************************/
 450 int BootSharedCommand::process(SharedOrderVector* order) {
 451         try{
 452                         /*      EstOutput data;
 453                                 vector<SharedRAbundVector*> subset;
 454
 455                                 //open an ostream for each calc to print to
 456                                 for (int z = 0; z < treeCalculators.size(); z++) {
 457                                         //create a new filename
 458                                         outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
 459                                         m->openOutputFile(outputFile, *(out[z]));
 460                                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 461                                 }
 462
 463                                 m->mothurOut("Generating bootstrap trees..."); cout.flush();
 464
 465                                 //create a file for each calculator with the 1000 trees in it.
 466                                 for (int p = 0; p < iters; p++) {
 467
 468                                         if (m->control_pressed) {  return 1; }
 469
 470                                         util->getSharedVectorswithReplacement(m->Groups, lookup, order);  //fills group vectors from order vector.
 471
 472
 473                                         //for each calculator
 474                                         for(int i = 0 ; i < treeCalculators.size(); i++) {
 475
 476                                                 if (m->control_pressed) {  return 1; }
 477
 478                                                 //initialize simMatrix
 479                                                 simMatrix.clear();
 480                                                 simMatrix.resize(numGroups);
 481                                                 for (int o = 0; o < simMatrix.size(); o++)      {
 482                                                         for (int j = 0; j < simMatrix.size(); j++)      {
 483                                                                 simMatrix[o].push_back(0.0);
 484                                                         }
 485                                                 }
 486
 487                                                 //initialize index
 488                                                 index.clear();
 489                                                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 490
 491                                                 for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
 492                                                         for (int l = k; l < lookup.size(); l++) {
 493                                                                 if (k != l) { //we dont need to similiarity of a groups to itself
 494                                                                         subset.clear(); //clear out old pair of sharedrabunds
 495                                                                         //add new pair of sharedrabunds
 496                                                                         subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 497
 498                                                                         //get estimated similarity between 2 groups
 499                                                                         data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 500                                                                         //save values in similarity matrix
 501                                                                         simMatrix[k][l] = data[0];
 502                                                                         simMatrix[l][k] = data[0];
 503                                                                 }
 504                                                         }
 505                                                 }
 506
 507                                                 tempTree = new Tree();
 508
 509                                                 if (m->control_pressed) {   delete tempTree; return 1; }
 510
 511                                                 //creates tree from similarity matrix and write out file
 512                                                 createTree(out[i], tempTree);
 513
 514                                                 if (m->control_pressed) {   delete tempTree; return 1; }
 515
 516                                                 //save trees for consensus command.
 517                                                 trees[i].push_back(tempTree);
 518                                         }
 519                                 }
 520
 521                                 m->mothurOut("\tDone."); m->mothurOutEndLine();
 522
 523
 524                                 //create consensus trees for each bootstrapped tree set
 525                                 for (int k = 0; k < trees.size(); k++) {
 526
 527                                         m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
 528
 529                                         if (m->control_pressed) {  return 1; }
 530
 531                                         //set global data to calc trees
 532                                         globaldata->gTree = trees[k];
 533
 534                                         string filename = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
 535                                         consensus = new ConcensusCommand(filename);
 536                                         consensus->execute();
 537                                         delete consensus;
 538
 539                                         outputNames.push_back(filename + ".cons.pairs");
 540                                         outputNames.push_back(filename + ".cons.tre");
 541
 542                                 }
 543
 544
 545
 546                                 //close ostream for each calc
 547                                 for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
 548                                 */
 549                                 return 0;
 550
 551         }
 552         catch(exception& e) {
 553                 m->errorOut(e, "BootSharedCommand", "process");
 554                 exit(1);
 555         }
 556 }
 557 /***********************************************************/
 558
 559
 560