unifracweightedcommand.cpp

   1 /*
   2  *  unifracweightedcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "unifracweightedcommand.h"
  11
  12 /***********************************************************/
  13 UnifracWeightedCommand::UnifracWeightedCommand() {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16
  17                 T = globaldata->gTree;
  18                 tmap = globaldata->gTreemap;
  19                 sumFile = globaldata->getTreeFile() + ".wsummary";
  20                 openOutputFile(sumFile, outSum);
  21
  22                 setGroups();    //sets the groups the user wants to analyze
  23                 convert(globaldata->getIters(), iters);  //how many random trees to generate
  24                 weighted = new Weighted(tmap);
  25
  26         }
  27         catch(exception& e) {
  28                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  29                 exit(1);
  30         }
  31         catch(...) {
  32                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  33                 exit(1);
  34         }
  35 }
  36 /***********************************************************/
  37 int UnifracWeightedCommand::execute() {
  38         try {
  39                 Progress* reading;
  40                 reading = new Progress("Comparing to random:", iters);
  41
  42                 //get weighted for users tree
  43                 userData.resize(numComp,0);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
  44                 randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
  45
  46                 //create new tree with same num nodes and leaves as users
  47                 randT = new Tree();
  48
  49                 //get weighted scores for users trees
  50                 for (int i = 0; i < T.size(); i++) {
  51                         counter = 0;
  52                         rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
  53                         uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
  54                         weightedFile = globaldata->getTreeFile()  + toString(i+1) + ".weighted";
  55                         weightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".weighted";
  56
  57                         userData = weighted->getValues(T[i]);  //userData[0] = weightedscore
  58
  59                         //save users score
  60                         for (int s=0; s<numComp; s++) {
  61                                 //add users score to vector of user scores
  62                                 uScores[s].push_back(userData[s]);
  63
  64                                 //save users tree score for summary file
  65                                 utreeScores.push_back(userData[s]);
  66                         }
  67
  68                         //get scores for random trees
  69                         for (int j = 0; j < iters; j++) {
  70                                 int count = 0;
  71                                 for (int r=0; r<numGroups; r++) {
  72                                         for (int l = r+1; l < numGroups; l++) {
  73                                                 //copy T[i]'s info.
  74                                                 randT->getCopy(T[i]);
  75
  76                                                 //create a random tree with same topology as T[i], but different labels
  77                                                 randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
  78                                                 //get wscore of random tree
  79                                                 randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
  80
  81                                                 //save scores
  82                                                 rScores[count].push_back(randomData[0]);
  83                                                 count++;
  84                                         }
  85                                 }
  86
  87                                 //update progress bar
  88                                 reading->update(j);
  89
  90                         }
  91
  92                         //removeValidScoresDuplicates();
  93                         //find the signifigance of the score for summary file
  94                         for (int f = 0; f < numComp; f++) {
  95                                 //sort random scores
  96                                 sort(rScores[f].begin(), rScores[f].end());
  97
  98                                 //the index of the score higher than yours is returned
  99                                 //so if you have 1000 random trees the index returned is 100
 100                                 //then there are 900 trees with a score greater then you.
 101                                 //giving you a signifigance of 0.900
 102                                 int index = findIndex(userData[f], f);    if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code
 103
 104                                 //the signifigance is the number of trees with the users score or higher
 105                                 WScoreSig.push_back((iters-index)/(float)iters);
 106                         }
 107
 108                         //out << "Tree# " << i << endl;
 109                         calculateFreqsCumuls();
 110                         printWeightedFile();
 111
 112                         //clear data
 113                         rScores.clear();
 114                         uScores.clear();
 115                         validScores.clear();
 116                 }
 117
 118                 //finish progress bar
 119                 reading->finish();
 120                 delete reading;
 121
 122                 printWSummaryFile();
 123
 124                 //clear out users groups
 125                 globaldata->Groups.clear();
 126
 127                 delete randT;
 128
 129                 return 0;
 130
 131         }
 132         catch(exception& e) {
 133                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 134                 exit(1);
 135         }
 136         catch(...) {
 137                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 138                 exit(1);
 139         }
 140 }
 141 /***********************************************************/
 142 void UnifracWeightedCommand::printWeightedFile() {
 143         try {
 144                 vector<double> data;
 145
 146                 for(int a = 0; a < numComp; a++) {
 147                         initFile(groupComb[a]);
 148                         //print each line
 149                         for (it = validScores.begin(); it != validScores.end(); it++) {
 150                                 data.push_back(it->first);  data.push_back(rScoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 151                                 output(data);
 152                                 data.clear();
 153                         }
 154                         resetFile();
 155                 }
 156
 157                 out.close();
 158                 inFile.close();
 159                 remove(weightedFileout.c_str());
 160
 161         }
 162         catch(exception& e) {
 163                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 164                 exit(1);
 165         }
 166         catch(...) {
 167                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 168                 exit(1);
 169         }
 170 }
 171
 172
 173 /***********************************************************/
 174 void UnifracWeightedCommand::printWSummaryFile() {
 175         try {
 176                 //column headers
 177                 outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
 178                 cout << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
 179
 180                 //format output
 181                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 182
 183                 //print each line
 184                 int count = 0;
 185                 for (int i = 0; i < T.size(); i++) {
 186                         for (int j = 0; j < numComp; j++) {
 187                                 if (WScoreSig[count] > (1/(float)iters)) {
 188                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl;
 189                                         cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl;
 190                                 }else{
 191                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
 192                                         cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
 193                                 }
 194                                 count++;
 195                         }
 196                 }
 197                 outSum.close();
 198         }
 199         catch(exception& e) {
 200                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 201                 exit(1);
 202         }
 203         catch(...) {
 204                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 205                 exit(1);
 206         }
 207 }
 208
 209 /***********************************************************/
 210 int UnifracWeightedCommand::findIndex(float score, int index) {
 211         try{
 212                 for (int i = 0; i < rScores[index].size(); i++) {
 213                         if (rScores[index][i] >= score) {       return i;       }
 214                 }
 215                 return rScores[index].size();
 216         }
 217         catch(exception& e) {
 218                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 219                 exit(1);
 220         }
 221         catch(...) {
 222                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 223                 exit(1);
 224         }
 225 }
 226
 227 /***********************************************************/
 228 void UnifracWeightedCommand::setGroups() {
 229         try {
 230                 numGroups = 0;
 231                 //if the user has not entered specific groups to analyze then do them all
 232                 if (globaldata->Groups.size() == 0) {
 233                         for (int i=0; i < tmap->getNumGroups(); i++) {
 234                                 if (tmap->namesOfGroups[i] != "xxx") {
 235                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 236                                         numGroups++;
 237                                 }
 238                         }
 239                 }else {
 240                         if (globaldata->getGroups() != "all") {
 241                                 //check that groups are valid
 242                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 243                                         if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 244                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 245                                                 // erase the invalid group from globaldata->Groups
 246                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 247                                         }
 248                                 }
 249
 250                                 //if the user only entered invalid groups
 251                                 if (globaldata->Groups.size() == 0) {
 252                                         for (int i=0; i < tmap->getNumGroups(); i++) {
 253                                                 if (tmap->namesOfGroups[i] != "xxx") {
 254                                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 255                                                         numGroups++;
 256                                                 }
 257                                         }
 258                                         cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 259                                 }else if (globaldata->Groups.size() == 1) {
 260                                         cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 261                                         globaldata->Groups.clear();
 262                                         for (int i=0; i < tmap->getNumGroups(); i++) {
 263                                                 if (tmap->namesOfGroups[i] != "xxx") {
 264                                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 265                                                         numGroups++;
 266                                                 }
 267                                         }
 268                                 }else { numGroups = globaldata->Groups.size(); }
 269                         }else { //users wants all groups
 270                                 globaldata->Groups.clear();
 271                                 globaldata->setGroups("");
 272                                 for (int i=0; i < tmap->getNumGroups(); i++) {
 273                                         if (tmap->namesOfGroups[i] != "xxx") {
 274                                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 275                                                 numGroups++;
 276                                         }
 277                                 }
 278                         }
 279                 }
 280
 281                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 282                 numComp = 0;
 283                 for (int i=0; i<numGroups; i++) {
 284                         numComp += i;
 285                         for (int l = i+1; l < numGroups; l++) {
 286                                 //set group comparison labels
 287                                 groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
 288                         }
 289                 }
 290         }
 291         catch(exception& e) {
 292                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 293                 exit(1);
 294         }
 295         catch(...) {
 296                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 297                 exit(1);
 298         }
 299 }
 300
 301 /***********************************************************/
 302
 303 void UnifracWeightedCommand::calculateFreqsCumuls() {
 304         try {
 305                 //clear out old tree values
 306                 rScoreFreq.clear();
 307                 rScoreFreq.resize(numComp);
 308                 rCumul.clear();
 309                 rCumul.resize(numComp);
 310                 validScores.clear();
 311
 312                 //calculate frequency
 313                 for (int f = 0; f < numComp; f++) {
 314                         for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7...  you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
 315                                 validScores[rScores[f][i]] = rScores[f][i];
 316                                 it = rScoreFreq[f].find(rScores[f][i]);
 317                                 if (it != rScoreFreq[f].end()) {
 318                                         rScoreFreq[f][rScores[f][i]]++;
 319                                 }else{
 320                                         rScoreFreq[f][rScores[f][i]] = 1;
 321                                 }
 322                         }
 323                 }
 324
 325                 //calculate rcumul
 326                 for(int a = 0; a < numComp; a++) {
 327                         float rcumul = 1.0000;
 328                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 329                         for (it = validScores.begin(); it != validScores.end(); it++) {
 330                                 //make rscoreFreq map and rCumul
 331                                 it2 = rScoreFreq[a].find(it->first);
 332                                 rCumul[a][it->first] = rcumul;
 333                                 //get percentage of random trees with that info
 334                                 if (it2 != rScoreFreq[a].end()) {  rScoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 335                                 else { rScoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 336                         }
 337                 }
 338
 339         }
 340         catch(exception& e) {
 341                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 342                 exit(1);
 343         }
 344         catch(...) {
 345                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 346                 exit(1);
 347         }
 348
 349 }
 350
 351 /*****************************************************************/
 352
 353 void UnifracWeightedCommand::initFile(string label){
 354         try {
 355                 if(counter != 0){
 356                         openOutputFile(weightedFileout, out);
 357                         openInputFile(weightedFile, inFile);
 358
 359                         string inputBuffer;
 360                         getline(inFile, inputBuffer);
 361
 362                         out     <<  inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 363                 }else{
 364                         openOutputFile(weightedFileout, out);
 365                         out     << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 366                 }
 367
 368                 out.setf(ios::fixed, ios::floatfield);
 369                 out.setf(ios::showpoint);
 370         }
 371         catch(exception& e) {
 372                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 373                 exit(1);
 374         }
 375         catch(...) {
 376                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 377                 exit(1);
 378         }
 379 }
 380
 381 /***********************************************************************/
 382
 383 void UnifracWeightedCommand::output(vector<double> data){
 384         try {
 385                 if(counter != 0){
 386                         string inputBuffer;
 387                         getline(inFile, inputBuffer);
 388
 389                         out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 390                 }
 391                 else{
 392                         out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 393
 394                 }
 395
 396         }
 397         catch(exception& e) {
 398                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 399                 exit(1);
 400         }
 401         catch(...) {
 402                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 403                 exit(1);
 404         }
 405 };
 406
 407 /***********************************************************************/
 408
 409 void UnifracWeightedCommand::resetFile(){
 410         try {
 411                 if(counter != 0){
 412                         out.close();
 413                         inFile.close();
 414                 }
 415                 else{
 416                         out.close();
 417                 }
 418                 counter = 1;
 419
 420                 remove(weightedFile.c_str());
 421                 rename(weightedFileout.c_str(), weightedFile.c_str());
 422         }
 423         catch(exception& e) {
 424                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 425                 exit(1);
 426         }
 427         catch(...) {
 428                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 429                 exit(1);
 430         }
 431 }
 432