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                 sumFile = globaldata->getTreeFile() + ".uwsummary";
  20                 openOutputFile(sumFile, outSum);
  21
  22                 util = new SharedUtil();
  23                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");   //sets the groups the user wants to analyze
  24                 util->getCombos(groupComb, globaldata->Groups, numComp);
  25                 globaldata->setGroups("");
  26
  27                 //ABC
  28                 if (numComp != 1) {
  29                         groupComb.push_back(allGroups);
  30                         numComp++;
  31                 }
  32
  33
  34                 convert(globaldata->getIters(), iters);  //how many random trees to generate
  35                 unweighted = new Unweighted(tmap);
  36
  37         }
  38         catch(exception& e) {
  39                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  40                 exit(1);
  41         }
  42         catch(...) {
  43                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46 }
  47 /***********************************************************/
  48 int UnifracUnweightedCommand::execute() {
  49         try {
  50
  51                 userData.resize(numComp,0);  //data[0] = unweightedscore
  52                 randomData.resize(numComp,0); //data[0] = unweightedscore
  53                 //create new tree with same num nodes and leaves as users
  54
  55                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
  56                 cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" << '\t' << "UWSig" <<  endl;
  57
  58                 //get pscores for users trees
  59                 for (int i = 0; i < T.size(); i++) {
  60                         counter = 0;
  61
  62                         output = new ColumnFile(globaldata->getTreeFile()  + toString(i+1) + ".unweighted");
  63
  64                         outSum << i+1 << '\t';
  65                         cout << i+1 << '\t';
  66
  67                         //get unweighted for users tree
  68                         rscoreFreq.resize(numComp);
  69                         rCumul.resize(numComp);
  70                         utreeScores.resize(numComp);
  71                         UWScoreSig.resize(numComp);
  72
  73                         userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
  74
  75                         //output scores for each combination
  76                         for(int k = 0; k < numComp; k++) {
  77                                 //saves users score
  78                                 utreeScores[k].push_back(userData[k]);
  79
  80                         }
  81
  82                         //get unweighted scores for random trees
  83                         for (int j = 0; j < iters; j++) {
  84                                 //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
  85                                 randomData = unweighted->getValues(T[i], "", "");
  86
  87                                 for(int k = 0; k < numComp; k++) {
  88                                         //add trees unweighted score to map of scores
  89                                         it2 = rscoreFreq[k].find(randomData[k]);
  90                                         if (it2 != rscoreFreq[k].end()) {//already have that score
  91                                                 rscoreFreq[k][randomData[k]]++;
  92                                         }else{//first time we have seen this score
  93                                                 rscoreFreq[k][randomData[k]] = 1;
  94                                         }
  95
  96                                         //add randoms score to validscores
  97                                         validScores[randomData[k]] = randomData[k];
  98                                 }
  99
 100                         }
 101
 102                         for(int a = 0; a < numComp; a++) {
 103                                 float rcumul = 1.0000;
 104                                 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 105                                 for (it = validScores.begin(); it != validScores.end(); it++) {
 106                                         //make rscoreFreq map and rCumul
 107                                         it2 = rscoreFreq[a].find(it->first);
 108                                         rCumul[a][it->first] = rcumul;
 109                                         //get percentage of random trees with that info
 110                                         if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 111                                         else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 112                                 }
 113                                 UWScoreSig[a].push_back(rCumul[a][userData[a]]);
 114                         }
 115
 116
 117
 118                         printUnweightedFile();
 119                         printUWSummaryFile();
 120
 121                         delete output;
 122                         rscoreFreq.clear();
 123                         rCumul.clear();
 124                         validScores.clear();
 125                         utreeScores.clear();
 126                         UWScoreSig.clear();
 127                 }
 128
 129                 //reset groups parameter
 130                 globaldata->Groups.clear();
 131                 outSum.close();
 132
 133                 return 0;
 134
 135         }
 136         catch(exception& e) {
 137                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 138                 exit(1);
 139         }
 140         catch(...) {
 141                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144 }
 145 /***********************************************************/
 146 void UnifracUnweightedCommand::printUnweightedFile() {
 147         try {
 148                 vector<double> data;
 149                 vector<string> tags;
 150                 tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 151
 152                 for(int a = 0; a < numComp; a++) {
 153                         output->initFile(groupComb[a], tags);
 154                         //print each line
 155                         for (it = validScores.begin(); it != validScores.end(); it++) {
 156                                 data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 157                                 output->output(data);
 158                                 data.clear();
 159                         }
 160                         output->resetFile();
 161                 }
 162         }
 163         catch(exception& e) {
 164                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167         catch(...) {
 168                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 169                 exit(1);
 170         }
 171 }
 172
 173 /***********************************************************/
 174 void UnifracUnweightedCommand::printUWSummaryFile() {
 175         try {
 176
 177                 //format output
 178                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 179
 180                 //print each line
 181
 182                 for(int a = 0; a < numComp; a++) {
 183                         if (UWScoreSig[a][0] > (1/(float)iters)) {
 184                                 outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
 185                                 cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
 186                         }else {
 187                                 outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
 188                                 cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
 189                         }
 190                 }
 191
 192         }
 193         catch(exception& e) {
 194                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 195                 exit(1);
 196         }
 197         catch(...) {
 198                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 199                 exit(1);
 200         }
 201 }
 202
 203 /***********************************************************/
 204
 205