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
  25 BootSharedCommand::BootSharedCommand(string option){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 abort = false;
  29                 allLines = 1;
  30                 labels.clear();
  31                 Groups.clear();
  32                 Estimators.clear();
  33
  34                 //allow user to run help
  35                 if(option == "help") { help(); abort = true; }
  36
  37                 else {
  38                         //valid paramters for this command
  39                         string Array[] =  {"label","calc","groups","iters"};
  40                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  41
  42                         OptionParser parser(option);
  43                         map<string,string> parameters = parser.getParameters();
  44
  45                         ValidParameters validParameter;
  46
  47                         //check to make sure all parameters are valid for command
  48                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  49                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  50                         }
  51
  52                         //make sure the user has already run the read.otu command
  53                         if (globaldata->getSharedFile() == "") {
  54                                 if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); mothurOutEndLine(); abort = true; }
  55                                 else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); mothurOutEndLine(); abort = true; }
  56                         }
  57
  58                         //check for optional parameter and set defaults
  59                         // ...at some point should added some additional type checking...
  60                         label = validParameter.validFile(parameters, "label", false);
  61                         if (label == "not found") { label = ""; }
  62                         else {
  63                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  64                                 else { allLines = 1;  }
  65                         }
  66
  67                         //if the user has not specified any labels use the ones from read.otu
  68                         if(label == "") {
  69                                 allLines = globaldata->allLines;
  70                                 labels = globaldata->labels;
  71                         }
  72
  73                         groups = validParameter.validFile(parameters, "groups", false);
  74                         if (groups == "not found") { groups = ""; }
  75                         else {
  76                                 splitAtDash(groups, Groups);
  77                                 globaldata->Groups = Groups;
  78                         }
  79
  80                         calc = validParameter.validFile(parameters, "calc", false);
  81                         if (calc == "not found") { calc = "jclass-thetayc";  }
  82                         else {
  83                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
  84                         }
  85                         splitAtDash(calc, Estimators);
  86
  87                         string temp;
  88                         temp = validParameter.validFile(parameters, "iters", false);  if (temp == "not found") { temp = "1000"; }
  89                         convert(temp, iters);
  90
  91                         if (abort == false) {
  92
  93                                 //used in tree constructor
  94                                 globaldata->runParse = false;
  95
  96                                 validCalculator = new ValidCalculators();
  97
  98                                 int i;
  99                                 for (i=0; i<Estimators.size(); i++) {
 100                                         if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
 101                                                 if (Estimators[i] == "jabund") {
 102                                                         treeCalculators.push_back(new JAbund());
 103                                                 }else if (Estimators[i] == "sorabund") {
 104                                                         treeCalculators.push_back(new SorAbund());
 105                                                 }else if (Estimators[i] == "jclass") {
 106                                                         treeCalculators.push_back(new Jclass());
 107                                                 }else if (Estimators[i] == "sorclass") {
 108                                                         treeCalculators.push_back(new SorClass());
 109                                                 }else if (Estimators[i] == "jest") {
 110                                                         treeCalculators.push_back(new Jest());
 111                                                 }else if (Estimators[i] == "sorest") {
 112                                                         treeCalculators.push_back(new SorEst());
 113                                                 }else if (Estimators[i] == "thetayc") {
 114                                                         treeCalculators.push_back(new ThetaYC());
 115                                                 }else if (Estimators[i] == "thetan") {
 116                                                         treeCalculators.push_back(new ThetaN());
 117                                                 }else if (Estimators[i] == "morisitahorn") {
 118                                                         treeCalculators.push_back(new MorHorn());
 119                                                 }else if (Estimators[i] == "braycurtis") {
 120                                                         treeCalculators.push_back(new BrayCurtis());
 121                                                 }
 122                                         }
 123                                 }
 124
 125                                 delete validCalculator;
 126
 127                                 ofstream* tempo;
 128                                 for (int i=0; i < treeCalculators.size(); i++) {
 129                                         tempo = new ofstream;
 130                                         out.push_back(tempo);
 131                                 }
 132
 133                                 //make a vector of tree* for each calculator
 134                                 trees.resize(treeCalculators.size());
 135                         }
 136                 }
 137
 138         }
 139         catch(exception& e) {
 140                 errorOut(e, "BootSharedCommand", "BootSharedCommand");
 141                 exit(1);
 142         }
 143 }
 144
 145 //**********************************************************************************************************************
 146
 147 void BootSharedCommand::help(){
 148         try {
 149                 mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n");
 150                 mothurOut("The bootstrap.shared command parameters are groups, calc, iters and label.\n");
 151                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
 152                 mothurOut("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");
 153                 mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n");
 154                 mothurOut("Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n");
 155                 mothurOut("The default value for groups is all the groups in your groupfile.\n");
 156                 mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n");
 157         }
 158         catch(exception& e) {
 159                 errorOut(e, "BootSharedCommand", "help");
 160                 exit(1);
 161         }
 162 }
 163
 164 //**********************************************************************************************************************
 165
 166 BootSharedCommand::~BootSharedCommand(){
 167         //made new in execute
 168         if (abort == false) {
 169                 delete input; globaldata->ginput = NULL;
 170                 delete read;
 171                 delete util;
 172                 globaldata->gorder = NULL;
 173         }
 174 }
 175
 176 //**********************************************************************************************************************
 177
 178 int BootSharedCommand::execute(){
 179         try {
 180
 181                 if (abort == true) {    return 0;       }
 182
 183                 util = new SharedUtil();
 184
 185                 //read first line
 186                 read = new ReadOTUFile(globaldata->inputFileName);
 187                 read->read(&*globaldata);
 188                 input = globaldata->ginput;
 189                 order = input->getSharedOrderVector();
 190                 string lastLabel = order->getLabel();
 191
 192                 //if the users entered no valid calculators don't execute command
 193                 if (treeCalculators.size() == 0) { return 0; }
 194
 195                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 196                 set<string> processedLabels;
 197                 set<string> userLabels = labels;
 198
 199                 //set users groups
 200                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
 201                 numGroups = globaldata->Groups.size();
 202
 203                 //clear globaldatas old tree names if any
 204                 globaldata->Treenames.clear();
 205
 206                 //fills globaldatas tree names
 207                 globaldata->Treenames = globaldata->Groups;
 208
 209                 //create treemap class from groupmap for tree class to use
 210                 tmap = new TreeMap();
 211                 tmap->makeSim(globaldata->gGroupmap);
 212                 globaldata->gTreemap = tmap;
 213
 214                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 215
 216                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 217
 218                                 mothurOut(order->getLabel()); mothurOutEndLine();
 219                                 process(order);
 220
 221                                 processedLabels.insert(order->getLabel());
 222                                 userLabels.erase(order->getLabel());
 223                         }
 224
 225                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 226                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 227
 228                                 delete order;
 229                                 order = input->getSharedOrderVector(lastLabel);
 230                                 mothurOut(order->getLabel()); mothurOutEndLine();
 231                                 process(order);
 232
 233                                 processedLabels.insert(order->getLabel());
 234                                 userLabels.erase(order->getLabel());
 235                         }
 236
 237
 238                         lastLabel = order->getLabel();
 239
 240                         //get next line to process
 241                         delete order;
 242                         order = input->getSharedOrderVector();
 243                 }
 244
 245                 //output error messages about any remaining user labels
 246                 set<string>::iterator it;
 247                 bool needToRun = false;
 248                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 249                         mothurOut("Your file does not include the label " + *it);
 250                         if (processedLabels.count(lastLabel) != 1) {
 251                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 252                                 needToRun = true;
 253                         }else {
 254                                 mothurOut(". Please refer to " + lastLabel + ".");  mothurOutEndLine();
 255                         }
 256                 }
 257
 258                 //run last line if you need to
 259                 if (needToRun == true)  {
 260                                 if (order != NULL) {    delete order;   }
 261                                 order = input->getSharedOrderVector(lastLabel);
 262                                 mothurOut(order->getLabel()); mothurOutEndLine();
 263                                 process(order);
 264                                 delete order;
 265
 266                 }
 267
 268                 //reset groups parameter
 269                 globaldata->Groups.clear();
 270
 271                 return 0;
 272         }
 273         catch(exception& e) {
 274                 errorOut(e, "BootSharedCommand", "execute");
 275                 exit(1);
 276         }
 277 }
 278 //**********************************************************************************************************************
 279
 280 void BootSharedCommand::createTree(ostream* out, Tree* t){
 281         try {
 282
 283                 //do merges and create tree structure by setting parents and children
 284                 //there are numGroups - 1 merges to do
 285                 for (int i = 0; i < (numGroups - 1); i++) {
 286
 287                         float largest = -1000.0;
 288                         int row, column;
 289                         //find largest value in sims matrix by searching lower triangle
 290                         for (int j = 1; j < simMatrix.size(); j++) {
 291                                 for (int k = 0; k < j; k++) {
 292                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 293                                 }
 294                         }
 295
 296                         //set non-leaf node info and update leaves to know their parents
 297                         //non-leaf
 298                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 299
 300                         //parents
 301                         t->tree[index[row]].setParent(numGroups + i);
 302                         t->tree[index[column]].setParent(numGroups + i);
 303
 304                         //blength = distance / 2;
 305                         float blength = ((1.0 - largest) / 2);
 306
 307                         //branchlengths
 308                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 309                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 310
 311                         //set your length to leaves to your childs length plus branchlength
 312                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 313
 314
 315                         //update index
 316                         index[row] = numGroups+i;
 317                         index[column] = numGroups+i;
 318
 319                         //zero out highest value that caused the merge.
 320                         simMatrix[row][column] = -1000.0;
 321                         simMatrix[column][row] = -1000.0;
 322
 323                         //merge values in simsMatrix
 324                         for (int n = 0; n < simMatrix.size(); n++)      {
 325                                 //row becomes merge of 2 groups
 326                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 327                                 simMatrix[n][row] = simMatrix[row][n];
 328                                 //delete column
 329                                 simMatrix[column][n] = -1000.0;
 330                                 simMatrix[n][column] = -1000.0;
 331                         }
 332                 }
 333
 334                 //adjust tree to make sure root to tip length is .5
 335                 int root = t->findRoot();
 336                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 337
 338                 //assemble tree
 339                 t->assembleTree();
 340
 341                 //print newick file
 342                 t->print(*out);
 343
 344         }
 345         catch(exception& e) {
 346                 errorOut(e, "BootSharedCommand", "createTree");
 347                 exit(1);
 348         }
 349 }
 350 /***********************************************************/
 351 void BootSharedCommand::printSims() {
 352         try {
 353                 mothurOut("simsMatrix"); mothurOutEndLine();
 354                 for (int m = 0; m < simMatrix.size(); m++)      {
 355                         for (int n = 0; n < simMatrix.size(); n++)      {
 356                                 mothurOut(simMatrix[m][n]);  mothurOut("\t");
 357                         }
 358                         mothurOutEndLine();
 359                 }
 360
 361         }
 362         catch(exception& e) {
 363                 errorOut(e, "BootSharedCommand", "printSims");
 364                 exit(1);
 365         }
 366 }
 367 /***********************************************************/
 368 void BootSharedCommand::process(SharedOrderVector* order) {
 369         try{
 370                                 EstOutput data;
 371                                 vector<SharedRAbundVector*> subset;
 372
 373
 374                                 //open an ostream for each calc to print to
 375                                 for (int z = 0; z < treeCalculators.size(); z++) {
 376                                         //create a new filename
 377                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
 378                                         openOutputFile(outputFile, *(out[z]));
 379                                 }
 380
 381                                 mothurOut("Generating bootstrap trees..."); cout.flush();
 382
 383                                 //create a file for each calculator with the 1000 trees in it.
 384                                 for (int p = 0; p < iters; p++) {
 385
 386                                         util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
 387
 388
 389                                         //for each calculator
 390                                         for(int i = 0 ; i < treeCalculators.size(); i++) {
 391
 392                                                 //initialize simMatrix
 393                                                 simMatrix.clear();
 394                                                 simMatrix.resize(numGroups);
 395                                                 for (int m = 0; m < simMatrix.size(); m++)      {
 396                                                         for (int j = 0; j < simMatrix.size(); j++)      {
 397                                                                 simMatrix[m].push_back(0.0);
 398                                                         }
 399                                                 }
 400
 401                                                 //initialize index
 402                                                 index.clear();
 403                                                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 404
 405                                                 for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
 406                                                         for (int l = k; l < lookup.size(); l++) {
 407                                                                 if (k != l) { //we dont need to similiarity of a groups to itself
 408                                                                         subset.clear(); //clear out old pair of sharedrabunds
 409                                                                         //add new pair of sharedrabunds
 410                                                                         subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 411
 412                                                                         //get estimated similarity between 2 groups
 413                                                                         data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 414                                                                         //save values in similarity matrix
 415                                                                         simMatrix[k][l] = data[0];
 416                                                                         simMatrix[l][k] = data[0];
 417                                                                 }
 418                                                         }
 419                                                 }
 420
 421                                                 tempTree = new Tree();
 422
 423                                                 //creates tree from similarity matrix and write out file
 424                                                 createTree(out[i], tempTree);
 425
 426                                                 //save trees for consensus command.
 427                                                 trees[i].push_back(tempTree);
 428                                         }
 429                                 }
 430
 431                                 mothurOut("\tDone."); mothurOutEndLine();
 432                                 //delete globaldata's tree
 433                                 //for (int m = 0; m < globaldata->gTree.size(); m++) {  delete globaldata->gTree[m];  }
 434                                 //globaldata->gTree.clear();
 435
 436
 437                                 //create consensus trees for each bootstrapped tree set
 438                                 for (int k = 0; k < trees.size(); k++) {
 439
 440                                         mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); mothurOutEndLine();
 441
 442                                         //set global data to calc trees
 443                                         globaldata->gTree = trees[k];
 444
 445                                         string filename = getRootName(globaldata->inputFileName) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
 446                                         consensus = new ConcensusCommand(filename);
 447                                         consensus->execute();
 448                                         delete consensus;
 449
 450                                         //delete globaldata's tree
 451                                         //for (int m = 0; m < globaldata->gTree.size(); m++) {  delete globaldata->gTree[m];  }
 452                                         //globaldata->gTree.clear();
 453
 454                                 }
 455
 456
 457
 458                                 //close ostream for each calc
 459                                 for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
 460
 461         }
 462         catch(exception& e) {
 463                 errorOut(e, "BootSharedCommand", "process");
 464                 exit(1);
 465         }
 466 }
 467 /***********************************************************/
 468
 469
 470