unifracunweightedcommand.cpp

   1 /*
   2  *  unifracunweightedcommand.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 "unifracunweightedcommand.h"
  11
  12 /***********************************************************/
  13 UnifracUnweightedCommand::UnifracUnweightedCommand() {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16
  17                 T = globaldata->gTree;
  18                 tmap = globaldata->gTreemap;
  19                 unweightedFile = globaldata->getTreeFile() + ".unweighted";
  20                 openOutputFile(unweightedFile, out);
  21                 sumFile = globaldata->getTreeFile() + ".uwsummary";
  22                 openOutputFile(sumFile, outSum);
  23                 distFile = globaldata->getTreeFile() + ".uwdistrib";
  24                 openOutputFile(distFile, outDist);
  25                 setGroups(); //sets users groups to analyze
  26                 convert(globaldata->getIters(), iters);  //how many random trees to generate
  27                 unweighted = new Unweighted(tmap);
  28
  29         }
  30         catch(exception& e) {
  31                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  32                 exit(1);
  33         }
  34         catch(...) {
  35                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  36                 exit(1);
  37         }
  38 }
  39 /***********************************************************/
  40 int UnifracUnweightedCommand::execute() {
  41         try {
  42
  43                 //get unweighted for users tree
  44                 userData.resize(1,0);  //data[0] = unweightedscore
  45                 randomData.resize(1,0); //data[0] = unweightedscore
  46
  47                 //format output
  48                 outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
  49
  50                 outDist << "Groups Used ";
  51                 for (int m = 0; m < globaldata->Groups.size(); m++) {
  52                         outDist << globaldata->Groups[m] << " ";
  53                 }
  54                 outDist << endl;
  55
  56                 outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
  57
  58                 //create new tree with same num nodes and leaves as users
  59                 randT = new Tree();
  60
  61                 //get pscores for users trees
  62                 for (int i = 0; i < T.size(); i++) {
  63                         cout << "Processing tree " << i+1 << endl;
  64                         userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
  65
  66                         //update uscoreFreq
  67                         it = uscoreFreq.find(userData[0]);
  68                         if (it == uscoreFreq.end()) {//new score
  69                                 uscoreFreq[userData[0]] = 1;
  70                         }else{ uscoreFreq[userData[0]]++; }
  71
  72                         //add users score to valid scores
  73                         validScores[userData[0]] = userData[0];
  74
  75                         //saves users score
  76                         utreeScores.push_back(userData[0]);
  77
  78                         //copy T[i]'s info.
  79                         randT->getCopy(T[i]);
  80
  81                         //get unweighted scores for random trees
  82                         for (int j = 0; j < iters; j++) {
  83                                 //create a random tree with same topology as T[i], but different labels
  84                                 randT->assembleRandomUnifracTree();
  85                                 //get pscore of random tree
  86                                 randomData = unweighted->getValues(randT);
  87
  88                                 //add trees unweighted score to map of scores
  89                                 it2 = rscoreFreq.find(randomData[0]);
  90                                 if (it2 != rscoreFreq.end()) {//already have that score
  91                                         rscoreFreq[randomData[0]]++;
  92                                 }else{//first time we have seen this score
  93                                         rscoreFreq[randomData[0]] = 1;
  94                                 }
  95
  96                                 //add randoms score to validscores
  97                                 validScores[randomData[0]] = randomData[0];
  98
  99                                 //output info to uwdistrib file
 100                                 outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
 101                         }
 102
 103                         saveRandomScores(); //save all random scores for unweighted file
 104
 105                         //find the signifigance of the score
 106                         float rcumul = 1.0000;
 107                         for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
 108                                 rCumul[it->first] = rcumul;
 109                                 //get percentage of random trees with that info
 110                                 rscoreFreq[it->first] /= iters;
 111                                 rcumul-= it->second;
 112
 113                         }
 114
 115                         //save the signifigance of the users score for printing later
 116                         UWScoreSig.push_back(rCumul[userData[0]]);
 117
 118
 119                         //clear random data
 120                         rscoreFreq.clear();  //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
 121                         rCumul.clear();
 122                 }
 123
 124                 float ucumul = 1.0000;
 125                 float rcumul = 1.0000;
 126                 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 127                 for (it = validScores.begin(); it != validScores.end(); it++) {
 128                         it2 = uscoreFreq.find(it->first);
 129                         //make uCumul map
 130                         uCumul[it->first] = ucumul;
 131                         //user data has that score
 132                         if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul-= it2->second;  }
 133                         else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
 134
 135                         //make rscoreFreq map and rCumul
 136                         it2 = totalrscoreFreq.find(it->first);
 137                         rCumul[it->first] = rcumul;
 138                         //get percentage of random trees with that info
 139                         if (it2 != totalrscoreFreq.end()) {  totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second;  }
 140                         else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
 141
 142                 }
 143
 144                 printUnweightedFile();
 145                 printUWSummaryFile();
 146
 147                 //reset groups parameter
 148                 globaldata->Groups.clear();
 149
 150                 delete randT;
 151
 152                 return 0;
 153
 154         }
 155         catch(exception& e) {
 156                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159         catch(...) {
 160                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163 }
 164 /***********************************************************/
 165 void UnifracUnweightedCommand::printUnweightedFile() {
 166         try {
 167                 //column headers
 168
 169                 out << "Groups Used ";
 170                 for (int m = 0; m < globaldata->Groups.size(); m++) {
 171                         out << globaldata->Groups[m] << " ";
 172                 }
 173                 out << endl;
 174
 175                 out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 176
 177                 //format output
 178                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 179
 180                 //print each line
 181                 for (it = validScores.begin(); it != validScores.end(); it++) {
 182                         out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << totalrscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
 183                 }
 184
 185                 out.close();
 186
 187         }
 188         catch(exception& e) {
 189                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 190                 exit(1);
 191         }
 192         catch(...) {
 193                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 194                 exit(1);
 195         }
 196 }
 197
 198 /***********************************************************/
 199 void UnifracUnweightedCommand::printUWSummaryFile() {
 200         try {
 201                 //column headers
 202
 203                 outSum << "Groups Used ";
 204                 for (int m = 0; m < globaldata->Groups.size(); m++) {
 205                         outSum << globaldata->Groups[m] << " ";
 206                 }
 207                 outSum << endl;
 208
 209                 outSum << "Tree#" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
 210
 211                 //format output
 212                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 213
 214                 //print each line
 215                 for (int i = 0; i< T.size(); i++) {
 216                         outSum << setprecision(6) << i+1 << '\t' << '\t' << utreeScores[i] << '\t' << UWScoreSig[i] << endl;
 217                 }
 218
 219                 outSum.close();
 220         }
 221         catch(exception& e) {
 222                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 223                 exit(1);
 224         }
 225         catch(...) {
 226                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 227                 exit(1);
 228         }
 229 }
 230 /***********************************************************/
 231 void UnifracUnweightedCommand::saveRandomScores() {
 232         try {
 233                 for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
 234                         //does this score already exist in the total map
 235                         it2 = totalrscoreFreq.find(it->first);
 236                         //if yes then add them
 237                         if (it2 != totalrscoreFreq.end()) {
 238                                 totalrscoreFreq[it->first] += rscoreFreq[it->first];
 239                         }else{ //its a new score
 240                                 totalrscoreFreq[it->first] = rscoreFreq[it->first];
 241                         }
 242                 }
 243         }
 244         catch(exception& e) {
 245                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 246                 exit(1);
 247         }
 248         catch(...) {
 249                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 250                 exit(1);
 251         }
 252 }
 253
 254 /***********************************************************/
 255
 256 void UnifracUnweightedCommand::setGroups() {
 257         try {
 258                 //if the user has not entered specific groups to analyze then do them all
 259                 if (globaldata->Groups.size() != 0) {
 260                         //check that groups are valid
 261                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 262                                 if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 263                                         cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 264                                         // erase the invalid group from globaldata->Groups
 265                                         globaldata->Groups.erase (globaldata->Groups.begin()+i);
 266                                 }
 267                         }
 268
 269                         //if the user only entered invalid groups
 270                         if (globaldata->Groups.size() == 0) {
 271                                 cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
 272                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 273                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 274                                 }
 275                         }
 276
 277                 }else {
 278                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 279                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 280                         }
 281                 }
 282         }
 283         catch(exception& e) {
 284                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 285                 exit(1);
 286         }
 287         catch(...) {
 288                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 289                 exit(1);
 290         }
 291
 292 }
 293 /*****************************************************************/
 294