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                 //if the user has not entered specific groups to analyze then do them all
 231                 if (globaldata->Groups.size() == 0) {
 232                         numGroups = tmap->getNumGroups();
 233                         for (int i=0; i < numGroups; i++) {
 234                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 235                         }
 236                 }else {
 237                         if (globaldata->getGroups() != "all") {
 238                                 //check that groups are valid
 239                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 240                                         if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 241                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 242                                                 // erase the invalid group from globaldata->Groups
 243                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 244                                         }
 245                                 }
 246
 247                                 //if the user only entered invalid groups
 248                                 if (globaldata->Groups.size() == 0) {
 249                                         numGroups = tmap->getNumGroups();
 250                                         for (int i=0; i < numGroups; i++) {
 251                                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 252                                         }
 253                                         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;
 254                                 }else if (globaldata->Groups.size() == 1) {
 255                                         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;
 256                                         numGroups = tmap->getNumGroups();
 257                                         globaldata->Groups.clear();
 258                                         for (int i=0; i < numGroups; i++) {
 259                                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 260                                         }
 261                                 }else { numGroups = globaldata->Groups.size(); }
 262                         }else { //users wants all groups
 263                                 numGroups = tmap->getNumGroups();
 264                                 globaldata->Groups.clear();
 265                                 globaldata->setGroups("");
 266                                 for (int i=0; i < numGroups; i++) {
 267                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 268                                 }
 269                         }
 270                 }
 271
 272                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 273                 numComp = 0;
 274                 for (int i=0; i<numGroups; i++) {
 275                         numComp += i;
 276                         for (int l = i+1; l < numGroups; l++) {
 277                                 //set group comparison labels
 278                                 groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
 279                         }
 280                 }
 281         }
 282         catch(exception& e) {
 283                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 284                 exit(1);
 285         }
 286         catch(...) {
 287                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 288                 exit(1);
 289         }
 290 }
 291
 292 /***********************************************************/
 293
 294 void UnifracWeightedCommand::calculateFreqsCumuls() {
 295         try {
 296                 //clear out old tree values
 297                 rScoreFreq.clear();
 298                 rScoreFreq.resize(numComp);
 299                 rCumul.clear();
 300                 rCumul.resize(numComp);
 301                 validScores.clear();
 302
 303                 //calculate frequency
 304                 for (int f = 0; f < numComp; f++) {
 305                         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...
 306                                 validScores[rScores[f][i]] = rScores[f][i];
 307                                 it = rScoreFreq[f].find(rScores[f][i]);
 308                                 if (it != rScoreFreq[f].end()) {
 309                                         rScoreFreq[f][rScores[f][i]]++;
 310                                 }else{
 311                                         rScoreFreq[f][rScores[f][i]] = 1;
 312                                 }
 313                         }
 314                 }
 315
 316                 //calculate rcumul
 317                 for(int a = 0; a < numComp; a++) {
 318                         float rcumul = 1.0000;
 319                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 320                         for (it = validScores.begin(); it != validScores.end(); it++) {
 321                                 //make rscoreFreq map and rCumul
 322                                 it2 = rScoreFreq[a].find(it->first);
 323                                 rCumul[a][it->first] = rcumul;
 324                                 //get percentage of random trees with that info
 325                                 if (it2 != rScoreFreq[a].end()) {  rScoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 326                                 else { rScoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 327                         }
 328                 }
 329
 330         }
 331         catch(exception& e) {
 332                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 333                 exit(1);
 334         }
 335         catch(...) {
 336                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 337                 exit(1);
 338         }
 339
 340 }
 341
 342 /*****************************************************************/
 343
 344 void UnifracWeightedCommand::initFile(string label){
 345         try {
 346                 if(counter != 0){
 347                         openOutputFile(weightedFileout, out);
 348                         openInputFile(weightedFile, inFile);
 349
 350                         string inputBuffer;
 351                         getline(inFile, inputBuffer);
 352
 353                         out     <<  inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 354                 }else{
 355                         openOutputFile(weightedFileout, out);
 356                         out     << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 357                 }
 358
 359                 out.setf(ios::fixed, ios::floatfield);
 360                 out.setf(ios::showpoint);
 361         }
 362         catch(exception& e) {
 363                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 364                 exit(1);
 365         }
 366         catch(...) {
 367                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 368                 exit(1);
 369         }
 370 }
 371
 372 /***********************************************************************/
 373
 374 void UnifracWeightedCommand::output(vector<double> data){
 375         try {
 376                 if(counter != 0){
 377                         string inputBuffer;
 378                         getline(inFile, inputBuffer);
 379
 380                         out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 381                 }
 382                 else{
 383                         out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 384
 385                 }
 386
 387         }
 388         catch(exception& e) {
 389                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 390                 exit(1);
 391         }
 392         catch(...) {
 393                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 394                 exit(1);
 395         }
 396 };
 397
 398 /***********************************************************************/
 399
 400 void UnifracWeightedCommand::resetFile(){
 401         try {
 402                 if(counter != 0){
 403                         out.close();
 404                         inFile.close();
 405                 }
 406                 else{
 407                         out.close();
 408                 }
 409                 counter = 1;
 410
 411                 remove(weightedFile.c_str());
 412                 rename(weightedFileout.c_str(), weightedFile.c_str());
 413         }
 414         catch(exception& e) {
 415                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 416                 exit(1);
 417         }
 418         catch(...) {
 419                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 420                 exit(1);
 421         }
 422 }
 423