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") { m->mothurOut("shared is a required parameter.");  m->mothurOutEndLine(); sharedfile = ""; abort = true; }
 117                         else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 118
 119                         //if the user changes the output directory command factory will send this info to us in the output parameter
 120                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 121                                 outputDir = "";
 122                                 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 123                         }
 124
 125                         //check for optional parameter and set defaults
 126                         // ...at some point should added some additional type checking...
 127                         label = validParameter.validFile(parameters, "label", false);
 128                         if (label == "not found") { label = ""; }
 129                         else {
 130                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 131                                 else { allLines = 1;  }
 132                         }
 133
 134                         groups = validParameter.validFile(parameters, "groups", false);
 135                         if (groups == "not found") { groups = ""; }
 136                         else {
 137                                 m->splitAtDash(groups, Groups);
 138                                 m->Groups = Groups;
 139                         }
 140
 141                         calc = validParameter.validFile(parameters, "calc", false);
 142                         if (calc == "not found") { calc = "jclass-thetayc";  }
 143                         else {
 144                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 145                         }
 146                         m->splitAtDash(calc, Estimators);
 147                         if (m->inUsersGroups("citation", Estimators)) {
 148                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 149                                 //remove citation from list of calcs
 150                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 151                         }
 152
 153                         string temp;
 154                         temp = validParameter.validFile(parameters, "iters", false);  if (temp == "not found") { temp = "1000"; }
 155                         convert(temp, iters);
 156
 157                         if (abort == false) {
 158
 159                                 //used in tree constructor
 160                                 m->runParse = false;
 161
 162                                 validCalculator = new ValidCalculators();
 163
 164
 165                                 //NOTE: if you add a calc to this if statement you must add it to the setParameters function
 166                                 //or it will not be visible in the gui
 167                                 int i;
 168                                 for (i=0; i<Estimators.size(); i++) {
 169                                         if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
 170                                                 if (Estimators[i] == "jabund") {
 171                                                         treeCalculators.push_back(new JAbund());
 172                                                 }else if (Estimators[i] == "sorabund") {
 173                                                         treeCalculators.push_back(new SorAbund());
 174                                                 }else if (Estimators[i] == "jclass") {
 175                                                         treeCalculators.push_back(new Jclass());
 176                                                 }else if (Estimators[i] == "sorclass") {
 177                                                         treeCalculators.push_back(new SorClass());
 178                                                 }else if (Estimators[i] == "jest") {
 179                                                         treeCalculators.push_back(new Jest());
 180                                                 }else if (Estimators[i] == "sorest") {
 181                                                         treeCalculators.push_back(new SorEst());
 182                                                 }else if (Estimators[i] == "thetayc") {
 183                                                         treeCalculators.push_back(new ThetaYC());
 184                                                 }else if (Estimators[i] == "thetan") {
 185                                                         treeCalculators.push_back(new ThetaN());
 186                                                 }else if (Estimators[i] == "morisitahorn") {
 187                                                         treeCalculators.push_back(new MorHorn());
 188                                                 }else if (Estimators[i] == "braycurtis") {
 189                                                         treeCalculators.push_back(new BrayCurtis());
 190                                                 }
 191                                         }
 192                                 }
 193
 194                                 delete validCalculator;
 195
 196                                 ofstream* tempo;
 197                                 for (int i=0; i < treeCalculators.size(); i++) {
 198                                         tempo = new ofstream;
 199                                         out.push_back(tempo);
 200                                 }
 201
 202                                 //make a vector of tree* for each calculator
 203                                 trees.resize(treeCalculators.size());
 204                         }
 205                 }
 206
 207         }
 208         catch(exception& e) {
 209                 m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
 210                 exit(1);
 211         }
 212 }
 213 //**********************************************************************************************************************
 214 BootSharedCommand::~BootSharedCommand(){}
 215 //**********************************************************************************************************************
 216
 217 int BootSharedCommand::execute(){
 218         try {
 219
 220                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 221
 222                 m->mothurOut("bootstrap.shared command is no longer available."); m->mothurOutEndLine();
 223         /*
 224                 //read first line
 225                 input = new InputData(sharedfile, "sharedfile");
 226                 order = input->getSharedOrderVector();
 227                 string lastLabel = order->getLabel();
 228
 229                 //if the users entered no valid calculators don't execute command
 230                 if (treeCalculators.size() == 0) { return 0; }
 231
 232                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 233                 set<string> processedLabels;
 234                 set<string> userLabels = labels;
 235
 236                 //set users groups
 237                 util = new SharedUtil();
 238                 util->setGroups(m->Groups, m->namesOfGroups, "treegroup");
 239
 240                 numGroups = m->Groups.size();
 241
 242                 //clear globaldatas old tree names if any
 243                 globaldata->Treenames.clear();
 244
 245                 //fills globaldatas tree names
 246                 globaldata->Treenames = m->Groups;
 247
 248                 //create treemap class from groupmap for tree class to use
 249                 tmap = new TreeMap();
 250                 tmap->makeSim(globaldata->gGroupmap);
 251                 globaldata->gTreemap = tmap;
 252
 253                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 254                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); delete input;delete util; return 0;      }
 255
 256                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 257
 258                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 259                                 int error = process(order);
 260                                 if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); delete input;delete util; return 0;      }
 261
 262                                 processedLabels.insert(order->getLabel());
 263                                 userLabels.erase(order->getLabel());
 264                         }
 265
 266                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 267                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 268                                 string saveLabel = order->getLabel();
 269
 270                                 delete order;
 271                                 order = input->getSharedOrderVector(lastLabel);
 272                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 273                                 int error = process(order);
 274                                 if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); delete input;delete util; return 0;      }
 275
 276                                 processedLabels.insert(order->getLabel());
 277                                 userLabels.erase(order->getLabel());
 278
 279                                 //restore real lastlabel to save below
 280                                 order->setLabel(saveLabel);
 281                         }
 282
 283
 284                         lastLabel = order->getLabel();
 285
 286                         //get next line to process
 287                         delete order;
 288                         order = input->getSharedOrderVector();
 289                 }
 290
 291
 292                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); delete input; delete util;  return 0;    }
 293
 294                 //output error messages about any remaining user labels
 295                 set<string>::iterator it;
 296                 bool needToRun = false;
 297                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 298                         m->mothurOut("Your file does not include the label " + *it);
 299                         if (processedLabels.count(lastLabel) != 1) {
 300                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 301                                 needToRun = true;
 302                         }else {
 303                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 304                         }
 305                 }
 306
 307                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); delete input; delete util; return 0;     }
 308
 309                 //run last line if you need to
 310                 if (needToRun == true)  {
 311                                 if (order != NULL) {    delete order;   }
 312                                 order = input->getSharedOrderVector(lastLabel);
 313                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 314                                 int error = process(order);
 315                                 if (error == 1) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear(); delete input; delete util; return 0;     }
 316
 317                                 delete order;
 318
 319                 }
 320
 321                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } globaldata->Groups.clear();delete input; delete util; return 0;      }
 322
 323                 //reset groups parameter
 324                 globaldata->Groups.clear();
 325
 326                 //set first tree file as new current treefile
 327                 string currentTree = "";
 328                 itTypes = outputTypes.find("tree");
 329                 if (itTypes != outputTypes.end()) {
 330                         if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
 331                 }
 332
 333                 delete input;
 334                 delete util;
 335
 336                 m->mothurOutEndLine();
 337                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 338                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 339                 m->mothurOutEndLine();
 340 */
 341
 342                 return 0;
 343         }
 344         catch(exception& e) {
 345                 m->errorOut(e, "BootSharedCommand", "execute");
 346                 exit(1);
 347         }
 348 }
 349 //**********************************************************************************************************************
 350
 351 int BootSharedCommand::createTree(ostream* out, Tree* t){
 352         try {
 353                 /*
 354                 //do merges and create tree structure by setting parents and children
 355                 //there are numGroups - 1 merges to do
 356                 for (int i = 0; i < (numGroups - 1); i++) {
 357
 358                         if (m->control_pressed) {  return 1; }
 359
 360                         float largest = -1000.0;
 361                         int row, column;
 362                         //find largest value in sims matrix by searching lower triangle
 363                         for (int j = 1; j < simMatrix.size(); j++) {
 364                                 for (int k = 0; k < j; k++) {
 365                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 366                                 }
 367                         }
 368
 369                         //set non-leaf node info and update leaves to know their parents
 370                         //non-leaf
 371                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 372
 373                         //parents
 374                         t->tree[index[row]].setParent(numGroups + i);
 375                         t->tree[index[column]].setParent(numGroups + i);
 376
 377                         //blength = distance / 2;
 378                         float blength = ((1.0 - largest) / 2);
 379
 380                         //branchlengths
 381                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 382                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 383
 384                         //set your length to leaves to your childs length plus branchlength
 385                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 386
 387
 388                         //update index
 389                         index[row] = numGroups+i;
 390                         index[column] = numGroups+i;
 391
 392                         //zero out highest value that caused the merge.
 393                         simMatrix[row][column] = -1000.0;
 394                         simMatrix[column][row] = -1000.0;
 395
 396                         //merge values in simsMatrix
 397                         for (int n = 0; n < simMatrix.size(); n++)      {
 398                                 //row becomes merge of 2 groups
 399                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 400                                 simMatrix[n][row] = simMatrix[row][n];
 401                                 //delete column
 402                                 simMatrix[column][n] = -1000.0;
 403                                 simMatrix[n][column] = -1000.0;
 404                         }
 405                 }
 406
 407                 //adjust tree to make sure root to tip length is .5
 408                 int root = t->findRoot();
 409                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 410
 411                 //assemble tree
 412                 t->assembleTree();
 413
 414                 if (m->control_pressed) { return 1; }
 415
 416                 //print newick file
 417                 t->print(*out);*/
 418
 419                 return 0;
 420
 421         }
 422         catch(exception& e) {
 423                 m->errorOut(e, "BootSharedCommand", "createTree");
 424                 exit(1);
 425         }
 426 }
 427 /***********************************************************/
 428 void BootSharedCommand::printSims() {
 429         try {
 430                 m->mothurOut("simsMatrix"); m->mothurOutEndLine();
 431                 for (int k = 0; k < simMatrix.size(); k++)      {
 432                         for (int n = 0; n < simMatrix.size(); n++)      {
 433                                 m->mothurOut(toString(simMatrix[k][n]));  m->mothurOut("\t");
 434                         }
 435                         m->mothurOutEndLine();
 436                 }
 437
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "BootSharedCommand", "printSims");
 441                 exit(1);
 442         }
 443 }
 444 /***********************************************************/
 445 int BootSharedCommand::process(SharedOrderVector* order) {
 446         try{
 447                         /*      EstOutput data;
 448                                 vector<SharedRAbundVector*> subset;
 449
 450                                 //open an ostream for each calc to print to
 451                                 for (int z = 0; z < treeCalculators.size(); z++) {
 452                                         //create a new filename
 453                                         outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
 454                                         m->openOutputFile(outputFile, *(out[z]));
 455                                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 456                                 }
 457
 458                                 m->mothurOut("Generating bootstrap trees..."); cout.flush();
 459
 460                                 //create a file for each calculator with the 1000 trees in it.
 461                                 for (int p = 0; p < iters; p++) {
 462
 463                                         if (m->control_pressed) {  return 1; }
 464
 465                                         util->getSharedVectorswithReplacement(m->Groups, lookup, order);  //fills group vectors from order vector.
 466
 467
 468                                         //for each calculator
 469                                         for(int i = 0 ; i < treeCalculators.size(); i++) {
 470
 471                                                 if (m->control_pressed) {  return 1; }
 472
 473                                                 //initialize simMatrix
 474                                                 simMatrix.clear();
 475                                                 simMatrix.resize(numGroups);
 476                                                 for (int o = 0; o < simMatrix.size(); o++)      {
 477                                                         for (int j = 0; j < simMatrix.size(); j++)      {
 478                                                                 simMatrix[o].push_back(0.0);
 479                                                         }
 480                                                 }
 481
 482                                                 //initialize index
 483                                                 index.clear();
 484                                                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 485
 486                                                 for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
 487                                                         for (int l = k; l < lookup.size(); l++) {
 488                                                                 if (k != l) { //we dont need to similiarity of a groups to itself
 489                                                                         subset.clear(); //clear out old pair of sharedrabunds
 490                                                                         //add new pair of sharedrabunds
 491                                                                         subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 492
 493                                                                         //get estimated similarity between 2 groups
 494                                                                         data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 495                                                                         //save values in similarity matrix
 496                                                                         simMatrix[k][l] = data[0];
 497                                                                         simMatrix[l][k] = data[0];
 498                                                                 }
 499                                                         }
 500                                                 }
 501
 502                                                 tempTree = new Tree();
 503
 504                                                 if (m->control_pressed) {   delete tempTree; return 1; }
 505
 506                                                 //creates tree from similarity matrix and write out file
 507                                                 createTree(out[i], tempTree);
 508
 509                                                 if (m->control_pressed) {   delete tempTree; return 1; }
 510
 511                                                 //save trees for consensus command.
 512                                                 trees[i].push_back(tempTree);
 513                                         }
 514                                 }
 515
 516                                 m->mothurOut("\tDone."); m->mothurOutEndLine();
 517
 518
 519                                 //create consensus trees for each bootstrapped tree set
 520                                 for (int k = 0; k < trees.size(); k++) {
 521
 522                                         m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
 523
 524                                         if (m->control_pressed) {  return 1; }
 525
 526                                         //set global data to calc trees
 527                                         globaldata->gTree = trees[k];
 528
 529                                         string filename = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
 530                                         consensus = new ConcensusCommand(filename);
 531                                         consensus->execute();
 532                                         delete consensus;
 533
 534                                         outputNames.push_back(filename + ".cons.pairs");
 535                                         outputNames.push_back(filename + ".cons.tre");
 536
 537                                 }
 538
 539
 540
 541                                 //close ostream for each calc
 542                                 for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
 543                                 */
 544                                 return 0;
 545
 546         }
 547         catch(exception& e) {
 548                 m->errorOut(e, "BootSharedCommand", "process");
 549                 exit(1);
 550         }
 551 }
 552 /***********************************************************/
 553
 554
 555