treegroupscommand.cpp

   1 /*
   2  *  treegroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "treegroupscommand.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 TreeGroupCommand::TreeGroupCommand(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") { validCalculator = new ValidCalculators(); help(); abort = true; }
  36
  37                 else {
  38                         //valid paramters for this command
  39                         string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
  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                         //required parameters
  53                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  54                         if (phylipfile == "not open") { abort = true; }
  55                         else if (phylipfile == "not found") { phylipfile = ""; }
  56                         else {  format = "phylip";      }
  57
  58                         columnfile = validParameter.validFile(parameters, "column", true);
  59                         if (columnfile == "not open") { abort = true; }
  60                         else if (columnfile == "not found") { columnfile = ""; }
  61                         else {  format = "column";      }
  62
  63                         namefile = validParameter.validFile(parameters, "name", true);
  64                         if (namefile == "not open") { abort = true; }
  65                         else if (namefile == "not found") { namefile = ""; }
  66                         else {  globaldata->setNameFile(namefile);      }
  67
  68                         format = globaldata->getFormat();
  69
  70                         //error checking on files
  71                         if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); mothurOutEndLine(); abort = true; }
  72                         else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
  73
  74                         if (columnfile != "") {
  75                                 if (namefile == "") {  mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
  76                         }
  77
  78                         //check for optional parameter and set defaults
  79                         // ...at some point should added some additional type checking...
  80                         label = validParameter.validFile(parameters, "label", false);
  81                         if (label == "not found") { label = ""; }
  82                         else {
  83                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  84                                 else { allLines = 1;  }
  85                         }
  86
  87                         //if the user has not specified any labels use the ones from read.otu
  88                         if(label == "") {
  89                                 allLines = globaldata->allLines;
  90                                 labels = globaldata->labels;
  91                         }
  92
  93                         groups = validParameter.validFile(parameters, "groups", false);
  94                         if (groups == "not found") { groups = ""; }
  95                         else {
  96                                 splitAtDash(groups, Groups);
  97                                 globaldata->Groups = Groups;
  98                         }
  99
 100                         calc = validParameter.validFile(parameters, "calc", false);
 101                         if (calc == "not found") { calc = "jclass-thetayc";  }
 102                         else {
 103                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 104                         }
 105                         splitAtDash(calc, Estimators);
 106
 107                         string temp;
 108                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 109                         convert(temp, precision);
 110
 111                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 112                         convert(temp, cutoff);
 113                         cutoff += (5 / (precision * 10.0));
 114
 115
 116                         if (abort == false) {
 117
 118                                 validCalculator = new ValidCalculators();
 119
 120                                 if (format == "sharedfile") {
 121                                         int i;
 122                                         for (i=0; i<Estimators.size(); i++) {
 123                                                 if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
 124                                                         if (Estimators[i] == "jabund") {
 125                                                                 treeCalculators.push_back(new JAbund());
 126                                                         }else if (Estimators[i] == "sorabund") {
 127                                                                 treeCalculators.push_back(new SorAbund());
 128                                                         }else if (Estimators[i] == "jclass") {
 129                                                                 treeCalculators.push_back(new Jclass());
 130                                                         }else if (Estimators[i] == "sorclass") {
 131                                                                 treeCalculators.push_back(new SorClass());
 132                                                         }else if (Estimators[i] == "jest") {
 133                                                                 treeCalculators.push_back(new Jest());
 134                                                         }else if (Estimators[i] == "sorest") {
 135                                                                 treeCalculators.push_back(new SorEst());
 136                                                         }else if (Estimators[i] == "thetayc") {
 137                                                                 treeCalculators.push_back(new ThetaYC());
 138                                                         }else if (Estimators[i] == "thetan") {
 139                                                                 treeCalculators.push_back(new ThetaN());
 140                                                         }else if (Estimators[i] == "morisitahorn") {
 141                                                                 treeCalculators.push_back(new MorHorn());
 142                                                         }else if (Estimators[i] == "braycurtis") {
 143                                                                 treeCalculators.push_back(new BrayCurtis());
 144                                                         }
 145                                                 }
 146                                         }
 147                                 }
 148                         }
 149                 }
 150
 151         }
 152         catch(exception& e) {
 153                 errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 154                 exit(1);
 155         }
 156 }
 157
 158 //**********************************************************************************************************************
 159
 160 void TreeGroupCommand::help(){
 161         try {
 162                 mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
 163                 mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
 164                 mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
 165                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
 166                 mothurOut("The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
 167                 mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used.  If you use a column file the name filename is required. \n");
 168                 mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
 169                 mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
 170                 mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
 171                 mothurOut("The default value for groups is all the groups in your groupfile.\n");
 172                 mothurOut("The default value for calc is jclass-thetayc.\n");
 173                 mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
 174                 validCalculator->printCalc("treegroup", cout);
 175                 mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
 176                 mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
 177                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 178         }
 179         catch(exception& e) {
 180                 errorOut(e, "TreeGroupCommand", "help");
 181                 exit(1);
 182         }
 183 }
 184
 185
 186 //**********************************************************************************************************************
 187
 188 TreeGroupCommand::~TreeGroupCommand(){
 189         if (abort == false) {
 190
 191                 if (format == "sharedfile") { delete read;  delete input; globaldata->ginput = NULL;}
 192                 else { delete readMatrix;  delete matrix; delete list; }
 193                 delete tmap;
 194                 delete validCalculator;
 195         }
 196
 197 }
 198
 199 //**********************************************************************************************************************
 200
 201 int TreeGroupCommand::execute(){
 202         try {
 203
 204                 if (abort == true) { return 0; }
 205
 206                 if (format == "sharedfile") {
 207                         //if the users entered no valid calculators don't execute command
 208                         if (treeCalculators.size() == 0) { mothurOut("You have given no valid calculators."); mothurOutEndLine(); return 0; }
 209
 210                         //you have groups
 211                         read = new ReadOTUFile(globaldata->inputFileName);
 212                         read->read(&*globaldata);
 213
 214                         input = globaldata->ginput;
 215                         lookup = input->getSharedRAbundVectors();
 216                         lastLabel = lookup[0]->getLabel();
 217
 218                         if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups.  I cannot run the command."); mothurOutEndLine(); return 0; }
 219
 220                         //used in tree constructor
 221                         globaldata->runParse = false;
 222
 223                         //create tree file
 224                         makeSimsShared();
 225                 }else{
 226                         //read in dist file
 227                         filename = globaldata->inputFileName;
 228
 229                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 230                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 231
 232                         readMatrix->setCutoff(cutoff);
 233
 234                         if(namefile != ""){
 235                                 nameMap = new NameAssignment(namefile);
 236                                 nameMap->readMap();
 237                         }
 238                         else{
 239                                 nameMap = NULL;
 240                         }
 241
 242                         readMatrix->read(nameMap);
 243                         list = readMatrix->getListVector();
 244                         matrix = readMatrix->getMatrix();
 245
 246                         //make treemap
 247                         tmap = new TreeMap();
 248                         tmap->makeSim(list);
 249                         globaldata->gTreemap = tmap;
 250
 251                         globaldata->Groups = tmap->namesOfGroups;
 252
 253                         //clear globaldatas old tree names if any
 254                         globaldata->Treenames.clear();
 255
 256                         //fills globaldatas tree names
 257                         globaldata->Treenames = globaldata->Groups;
 258
 259                         //used in tree constructor
 260                         globaldata->runParse = false;
 261
 262                         makeSimsDist();
 263
 264                         //create a new filename
 265                         outputFile = getRootName(globaldata->inputFileName) + "tre";
 266
 267                         createTree();
 268                         mothurOut("Tree complete. "); mothurOutEndLine();
 269                 }
 270
 271                 //reset groups parameter
 272                 globaldata->Groups.clear();
 273
 274                 return 0;
 275         }
 276         catch(exception& e) {
 277                 errorOut(e, "TreeGroupCommand", "execute");
 278                 exit(1);
 279         }
 280 }
 281 //**********************************************************************************************************************
 282
 283 void TreeGroupCommand::createTree(){
 284         try {
 285                 //create tree
 286                 t = new Tree();
 287
 288                 //do merges and create tree structure by setting parents and children
 289                 //there are numGroups - 1 merges to do
 290                 for (int i = 0; i < (numGroups - 1); i++) {
 291                         float largest = -1000.0;
 292
 293                         int row, column;
 294                         //find largest value in sims matrix by searching lower triangle
 295                         for (int j = 1; j < simMatrix.size(); j++) {
 296                                 for (int k = 0; k < j; k++) {
 297                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 298                                 }
 299                         }
 300
 301                         //set non-leaf node info and update leaves to know their parents
 302                         //non-leaf
 303                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 304
 305                         //parents
 306                         t->tree[index[row]].setParent(numGroups + i);
 307                         t->tree[index[column]].setParent(numGroups + i);
 308
 309                         //blength = distance / 2;
 310                         float blength = ((1.0 - largest) / 2);
 311
 312                         //branchlengths
 313                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 314                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 315
 316                         //set your length to leaves to your childs length plus branchlength
 317                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 318
 319
 320                         //update index
 321                         index[row] = numGroups+i;
 322                         index[column] = numGroups+i;
 323
 324                         //remove highest value that caused the merge.
 325                         simMatrix[row][column] = -1000.0;
 326                         simMatrix[column][row] = -1000.0;
 327
 328                         //merge values in simsMatrix
 329                         for (int n = 0; n < simMatrix.size(); n++)      {
 330                                 //row becomes merge of 2 groups
 331                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 332                                 simMatrix[n][row] = simMatrix[row][n];
 333                                 //delete column
 334                                 simMatrix[column][n] = -1000.0;
 335                                 simMatrix[n][column] = -1000.0;
 336                         }
 337                 }
 338
 339                 //adjust tree to make sure root to tip length is .5
 340                 int root = t->findRoot();
 341                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 342
 343                 //assemble tree
 344                 t->assembleTree();
 345
 346                 //print newick file
 347                 t->createNewickFile(outputFile);
 348
 349                 //delete tree
 350                 delete t;
 351
 352         }
 353         catch(exception& e) {
 354                 errorOut(e, "TreeGroupCommand", "createTree");
 355                 exit(1);
 356         }
 357 }
 358 /***********************************************************/
 359 void TreeGroupCommand::printSims(ostream& out) {
 360         try {
 361
 362                 //output column headers
 363                 //out << '\t';
 364                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 365                 //out << endl;
 366
 367
 368                 for (int m = 0; m < simMatrix.size(); m++)      {
 369                         //out << lookup[m]->getGroup() << '\t';
 370                         for (int n = 0; n < simMatrix.size(); n++)      {
 371                                 out << simMatrix[m][n] << '\t';
 372                         }
 373                         out << endl;
 374                 }
 375
 376         }
 377         catch(exception& e) {
 378                 errorOut(e, "TreeGroupCommand", "printSims");
 379                 exit(1);
 380         }
 381 }
 382 /***********************************************************/
 383 void TreeGroupCommand::makeSimsDist() {
 384         try {
 385                 numGroups = list->size();
 386
 387                 //initialize index
 388                 index.clear();
 389                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 390
 391                 //initialize simMatrix
 392                 simMatrix.clear();
 393                 simMatrix.resize(numGroups);
 394                 for (int m = 0; m < simMatrix.size(); m++)      {
 395                         for (int j = 0; j < simMatrix.size(); j++)      {
 396                                 simMatrix[m].push_back(0.0);
 397                         }
 398                 }
 399
 400                 //go through sparse matrix and fill sims
 401                 //go through each cell in the sparsematrix
 402                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 403                         //similairity = -(distance-1)
 404                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 405                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 406                 }
 407
 408
 409         }
 410         catch(exception& e) {
 411                 errorOut(e, "TreeGroupCommand", "makeSimsDist");
 412                 exit(1);
 413         }
 414 }
 415
 416 /***********************************************************/
 417 void TreeGroupCommand::makeSimsShared() {
 418         try {
 419
 420                 //clear globaldatas old tree names if any
 421                 globaldata->Treenames.clear();
 422
 423                 //fills globaldatas tree names
 424                 globaldata->Treenames = globaldata->Groups;
 425
 426                 //create treemap class from groupmap for tree class to use
 427                 tmap = new TreeMap();
 428                 tmap->makeSim(globaldata->gGroupmap);
 429                 globaldata->gTreemap = tmap;
 430
 431                 set<string> processedLabels;
 432                 set<string> userLabels = labels;
 433
 434                 //as long as you are not at the end of the file or done wih the lines you want
 435                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 436
 437                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 438                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 439                                 process(lookup);
 440
 441                                 processedLabels.insert(lookup[0]->getLabel());
 442                                 userLabels.erase(lookup[0]->getLabel());
 443                         }
 444
 445                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 446                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 447                                 lookup = input->getSharedRAbundVectors(lastLabel);
 448
 449                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 450                                 process(lookup);
 451
 452                                 processedLabels.insert(lookup[0]->getLabel());
 453                                 userLabels.erase(lookup[0]->getLabel());
 454                         }
 455
 456                         lastLabel = lookup[0]->getLabel();
 457
 458                         //get next line to process
 459                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 460                         lookup = input->getSharedRAbundVectors();
 461                 }
 462
 463                 //output error messages about any remaining user labels
 464                 set<string>::iterator it;
 465                 bool needToRun = false;
 466                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 467                         mothurOut("Your file does not include the label " + *it);
 468                         if (processedLabels.count(lastLabel) != 1) {
 469                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 470                                 needToRun = true;
 471                         }else {
 472                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 473                         }
 474                 }
 475
 476                 //run last label if you need to
 477                 if (needToRun == true)  {
 478                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 479                         lookup = input->getSharedRAbundVectors(lastLabel);
 480
 481                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 482                         process(lookup);
 483                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 484                 }
 485
 486                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 487         }
 488         catch(exception& e) {
 489                 errorOut(e, "TreeGroupCommand", "makeSimsShared");
 490                 exit(1);
 491         }
 492 }
 493
 494 /***********************************************************/
 495 void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 496         try{
 497                                 EstOutput data;
 498                                 vector<SharedRAbundVector*> subset;
 499                                 numGroups = thisLookup.size();
 500
 501                                 //for each calculator
 502                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 503                                         //initialize simMatrix
 504                                         simMatrix.clear();
 505                                         simMatrix.resize(numGroups);
 506                                         for (int m = 0; m < simMatrix.size(); m++)      {
 507                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 508                                                         simMatrix[m].push_back(0.0);
 509                                                 }
 510                                         }
 511
 512                                         //initialize index
 513                                         index.clear();
 514                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 515
 516                                         //create a new filename
 517                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 518
 519                                         for (int k = 0; k < thisLookup.size(); k++) {
 520                                                 for (int l = k; l < thisLookup.size(); l++) {
 521                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 522                                                                 //get estimated similarity between 2 groups
 523
 524                                                                 subset.clear(); //clear out old pair of sharedrabunds
 525                                                                 //add new pair of sharedrabunds
 526                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 527
 528                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 529                                                                 //save values in similarity matrix
 530                                                                 simMatrix[k][l] = data[0];
 531                                                                 simMatrix[l][k] = data[0];
 532                                                         }
 533                                                 }
 534                                         }
 535
 536                                         //creates tree from similarity matrix and write out file
 537                                         createTree();
 538                                 }
 539
 540         }
 541         catch(exception& e) {
 542                 errorOut(e, "TreeGroupCommand", "process");
 543                 exit(1);
 544         }
 545 }
 546 /***********************************************************/
 547
 548
 549