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                 weightedFile = globaldata->getTreeFile() + ".weighted";
  20                 openOutputFile(weightedFile, out);
  21                 //column headers
  22                 out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
  23
  24                 sumFile = globaldata->getTreeFile() + ".wsummary";
  25                 openOutputFile(sumFile, outSum);
  26
  27                 setGroups();    //sets the groups the user wants to analyze
  28                 convert(globaldata->getIters(), iters);  //how many random trees to generate
  29                 weighted = new Weighted(tmap);
  30
  31         }
  32         catch(exception& e) {
  33                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36         catch(...) {
  37                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40 }
  41 /***********************************************************/
  42 int UnifracWeightedCommand::execute() {
  43         try {
  44
  45                 //get weighted for users tree
  46                 userData.resize(numComp,0);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
  47                 randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
  48
  49                 //create new tree with same num nodes and leaves as users
  50                 randT = new Tree();
  51
  52                 //get pscores for users trees
  53                 for (int i = 0; i < T.size(); i++) {
  54                         rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
  55                         uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
  56                         validScores.resize(numComp);
  57
  58                         cout << "Processing tree " << i+1 << endl;
  59                         userData = weighted->getValues(T[i]);  //userData[0] = weightedscore
  60
  61                         //save users score
  62                         for (int s=0; s<numComp; s++) {
  63                                 //add users score to vector of user scores
  64                                 uScores[s].push_back(userData[s]);
  65
  66                                 //add users score to vector of valid scores
  67                                 validScores[s].push_back(userData[s]);
  68
  69                                 //save users tree score for summary file
  70                                 utreeScores.push_back(userData[s]);
  71                         }
  72
  73                         //get scores for random trees
  74                         for (int j = 0; j < iters; j++) {
  75 //                              int n = 1;
  76                                 int count = 0;
  77                                 for (int r=0; r<numGroups; r++) {
  78                                         for (int l = r+1; l < numGroups; l++) {
  79                                                 //copy T[i]'s info.
  80                                                 randT->getCopy(T[i]);
  81
  82                                                 if (globaldata->Groups.size() != 0) {
  83                                                         //create a random tree with same topology as T[i], but different labels
  84                                                         randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
  85                                                         //get wscore of random tree
  86                                                         randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
  87                                                 }else {
  88                                                         //create a random tree with same topology as T[i], but different labels
  89                                                         randT->assembleRandomUnifracTree(tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
  90                                                         //get wscore of random tree
  91                                                         randomData = weighted->getValues(randT, tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
  92                                                 }
  93 //                                              randT->createNewickFile("hold"+toString(r)+toString(l)+toString(j));
  94
  95                                                 //save scores
  96                                                 rScores[count].push_back(randomData[0]);
  97                                                 validScores[count][randomData[0]] = randomData[0];
  98                                                 count++;
  99                                         }
 100 //                                      n++;
 101                                 }
 102                         }
 103
 104                         removeValidScoresDuplicates();
 105                         //find the signifigance of the score for summary file
 106                         for (int f = 0; f < numComp; f++) {
 107                                 //sort random scores
 108                                 sort(rScores[f].begin(), rScores[f].end());
 109
 110                                 //the index of the score higher than yours is returned
 111                                 //so if you have 1000 random trees the index returned is 100
 112                                 //then there are 900 trees with a score greater then you.
 113                                 //giving you a signifigance of 0.900
 114                                 int index = findIndex(userData[f], f);    if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code
 115
 116                                 //the signifigance is the number of trees with the users score or higher
 117                                 WScoreSig.push_back((iters-index)/(float)iters);
 118                         }
 119
 120                         out << "Tree# " << i << endl;
 121                         //printWeightedFile();
 122
 123                         //clear data
 124                         rScores.clear();
 125                         uScores.clear();
 126                         validScores.clear();
 127                 }
 128
 129                 printWSummaryFile();
 130
 131                 //clear out users groups
 132                 globaldata->Groups.clear();
 133
 134                 delete randT;
 135
 136                 return 0;
 137
 138         }
 139         catch(exception& e) {
 140                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 141                 exit(1);
 142         }
 143         catch(...) {
 144                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 145                 exit(1);
 146         }
 147 }
 148 /***********************************************************
 149 void UnifracWeightedCommand::printWeightedFile() {
 150         try {
 151
 152                 //format output
 153                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 154
 155                 //for each group
 156                 for (int e = 0; e < numComp; e++) {
 157                         //print each line in that group
 158                         for (i = 0; i < validScores[e].size(); i++) {
 159                                 out << setprecision(6) <<  groupComb[e] << '\t' << validScores[e][i] << '\t' << '\t' << uscoreFreq[e][it->first] << '\t' << uCumul[e][it->first] << '\t' << rscoreFreq[e][it->first] << '\t' << rCumul[e][it->first] << endl;
 160                         }
 161                 }
 162
 163                 out.close();
 164
 165         }
 166         catch(exception& e) {
 167                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 168                 exit(1);
 169         }
 170         catch(...) {
 171                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 172                 exit(1);
 173         }
 174 }
 175
 176
 177 /***********************************************************/
 178 void UnifracWeightedCommand::printWSummaryFile() {
 179         try {
 180                 //column headers
 181                 outSum << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" <<  endl;
 182                 cout << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" <<  endl;
 183
 184                 //format output
 185                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 186
 187                 //print each line
 188                 int count = 0;
 189                 for (int i = 0; i < T.size(); i++) {
 190                         for (int j = 0; j < numComp; j++) {
 191                                 outSum << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
 192                                 cout << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
 193                                 count++;
 194                         }
 195                 }
 196                 outSum.close();
 197         }
 198         catch(exception& e) {
 199                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202         catch(...) {
 203                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 204                 exit(1);
 205         }
 206 }
 207
 208 /***********************************************************/
 209 void UnifracWeightedCommand::removeValidScoresDuplicates() {
 210         try {
 211                 for (int e = 0; e < numComp; e++) {
 212                         //sort valid scores
 213                         sort(validScores[e].begin(), validScores[e].end());
 214
 215                         for (int i = 0; i< validScores[e].size()-1; i++) {
 216                                 if (validScores[e][i] == validScores[e][i+1]) { validScores[e].erase(validScores[e].begin()+i); }
 217                         }
 218                 }
 219         }
 220         catch(exception& e) {
 221                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function removeValidScoresDuplicates. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 222                 exit(1);
 223         }
 224         catch(...) {
 225                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function removeValidScoresDuplicates. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 226                 exit(1);
 227         }
 228 }
 229
 230 /***********************************************************/
 231 int UnifracWeightedCommand::findIndex(float score, int index) {
 232         try{
 233                 for (int i = 0; i < rScores[index].size(); i++) {
 234                         if (rScores[index][i] >= score) {       return i;       }
 235                 }
 236                 return rScores[index].size();
 237         }
 238         catch(exception& e) {
 239                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 240                 exit(1);
 241         }
 242         catch(...) {
 243                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 244                 exit(1);
 245         }
 246 }
 247
 248 /***********************************************************/
 249 void UnifracWeightedCommand::setGroups() {
 250         try {
 251                 //if the user has not entered specific groups to analyze then do them all
 252                 if (globaldata->Groups.size() == 0) {
 253                         numGroups = tmap->getNumGroups();
 254                 }else {
 255                         if (globaldata->getGroups() != "all") {
 256                                 //check that groups are valid
 257                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 258                                         if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 259                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 260                                                 // erase the invalid group from globaldata->Groups
 261                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 262                                         }
 263                                 }
 264
 265                                 //if the user only entered invalid groups
 266                                 if (globaldata->Groups.size() == 0) {
 267                                         numGroups = tmap->getNumGroups();
 268                                         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;
 269                                 }else if (globaldata->Groups.size() == 1) {
 270                                         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;
 271                                         numGroups = tmap->getNumGroups();
 272                                         globaldata->Groups.clear();
 273                                 }else { numGroups = globaldata->Groups.size(); }
 274                         }else { //users wants all groups
 275                                 numGroups = tmap->getNumGroups();
 276                                 globaldata->Groups.clear();
 277                                 globaldata->setGroups("");
 278                         }
 279                 }
 280
 281                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 282                 numComp = 0;
 283                 int n = 1;
 284                 for (int i=1; i<numGroups; i++) {
 285                         numComp += i;
 286                         for (int l = n; l < numGroups; l++) {
 287                                 //set group comparison labels
 288                                 if (globaldata->Groups.size() != 0) {
 289                                         groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
 290                                 }else {
 291                                         groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
 292                                 }
 293                         }
 294                         n++;
 295                 }
 296         }
 297         catch(exception& e) {
 298                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 299                 exit(1);
 300         }
 301         catch(...) {
 302                 cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 303                 exit(1);
 304         }
 305 }
 306