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                 setGroups(); //sets users groups to analyze
  23                 convert(globaldata->getIters(), iters);  //how many random trees to generate
  24                 unweighted = new Unweighted(tmap);
  25                 counter = 0;
  26
  27         }
  28         catch(exception& e) {
  29                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32         catch(...) {
  33                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36 }
  37 /***********************************************************/
  38 int UnifracUnweightedCommand::execute() {
  39         try {
  40
  41                 userData.resize(numComp,0);  //data[0] = unweightedscore
  42                 randomData.resize(numComp,0); //data[0] = unweightedscore
  43                 //create new tree with same num nodes and leaves as users
  44
  45                 //get pscores for users trees
  46                 for (int i = 0; i < T.size(); i++) {
  47                         unweightedFile = globaldata->getTreeFile()  + toString(i+1) + ".unweighted";
  48                         unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
  49                                                 //column headers
  50                         outSum << "Tree# " << i+1 << endl;
  51                         outSum << "Comb" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
  52
  53                         //get unweighted for users tree
  54                         rscoreFreq.resize(numComp);
  55                         rCumul.resize(numComp);
  56                         validScores.resize(numComp);
  57                         utreeScores.resize(numComp);
  58                         UWScoreSig.resize(numComp);
  59
  60                         cout << "Processing tree " << i+1 << endl;
  61                         userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
  62
  63                         //output scores for each combination
  64                         for(int k = 0; k < numComp; k++) {
  65                                 //add users score to valid scores
  66                                 validScores[k][userData[k]] = userData[k];
  67
  68                                 //saves users score
  69                                 utreeScores[k].push_back(userData[k]);
  70                         }
  71
  72                         //get unweighted scores for random trees
  73                         for (int j = 0; j < iters; j++) {
  74                                 //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
  75                                 randomData = unweighted->getValues(T[i], "", "");
  76
  77                                 for(int k = 0; k < numComp; k++) {
  78 //cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
  79                                         //add trees unweighted score to map of scores
  80                                         it2 = rscoreFreq[k].find(randomData[k]);
  81                                         if (it2 != rscoreFreq[k].end()) {//already have that score
  82                                                 rscoreFreq[k][randomData[k]]++;
  83                                         }else{//first time we have seen this score
  84                                                 rscoreFreq[k][randomData[k]] = 1;
  85                                         }
  86
  87                                         //add randoms score to validscores
  88                                         validScores[k][randomData[k]] = randomData[k];
  89                                 }
  90                         }
  91
  92                 for(int a = 0; a < numComp; a++) {
  93                         float rcumul = 1.0000;
  94                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
  95                         for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
  96                                 //make rscoreFreq map and rCumul
  97                                 it2 = rscoreFreq[a].find(it->first);
  98                                 rCumul[a][it->first] = rcumul;
  99                                 //get percentage of random trees with that info
 100                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 101                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 102                         }
 103                         UWScoreSig[a].push_back(rCumul[a][userData[a]]);
 104                 }
 105
 106                 printUnweightedFile();
 107                 printUWSummaryFile();
 108
 109                 rscoreFreq.clear();
 110                 rCumul.clear();
 111                 validScores.clear();
 112                 utreeScores.clear();
 113                 UWScoreSig.clear();
 114         }
 115                 //reset groups parameter
 116                 globaldata->Groups.clear(); globaldata->setGroups("");
 117                 outSum.close();
 118
 119                 return 0;
 120
 121         }
 122         catch(exception& e) {
 123                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126         catch(...) {
 127                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 128                 exit(1);
 129         }
 130 }
 131 /***********************************************************/
 132 void UnifracUnweightedCommand::printUnweightedFile() {
 133         try {
 134                 vector<double> data;
 135
 136                 for(int a = 0; a < numComp; a++) {
 137                         initFile(groupComb[a]);
 138                         //print each line
 139                         for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
 140                                 data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 141                                 output(data);
 142                                 data.clear();
 143                         }
 144                         resetFile();
 145                 }
 146
 147                 out.close();
 148                 inFile.close();
 149                 remove(unweightedFileout.c_str());
 150
 151         }
 152         catch(exception& e) {
 153                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 154                 exit(1);
 155         }
 156         catch(...) {
 157                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 158                 exit(1);
 159         }
 160 }
 161
 162 /***********************************************************/
 163 void UnifracUnweightedCommand::printUWSummaryFile() {
 164         try {
 165
 166                 //format output
 167                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 168
 169                 //print each line
 170                 for(int a = 0; a < numComp; a++) {
 171                         outSum << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
 172                         cout << setprecision(6)  << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
 173                 }
 174
 175         }
 176         catch(exception& e) {
 177                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 178                 exit(1);
 179         }
 180         catch(...) {
 181                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184 }
 185 /***********************************************************/
 186
 187 void UnifracUnweightedCommand::setGroups() {
 188         try {
 189                 string allGroups = "";
 190                 numGroups = 0;
 191                 //if the user has not entered specific groups to analyze then do them all
 192                 if (globaldata->Groups.size() != 0) {
 193                         if (globaldata->Groups[0] != "all") {
 194                                 //check that groups are valid
 195                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 196                                         if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 197                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 198                                                 // erase the invalid group from globaldata->Groups
 199                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 200                                         }
 201                                 }
 202
 203                                 //if the user only entered invalid groups
 204                                 if (globaldata->Groups.size() == 0) {
 205                                         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;
 206                                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 207                                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 208                                                 numGroups++;
 209                                                 allGroups += tmap->namesOfGroups[i];
 210                                         }
 211                                 }else {
 212                                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 213                                                 allGroups += globaldata->Groups[i];
 214                                                 numGroups++;
 215                                         }
 216                                 }
 217                         }else{//user has enter "all" and wants the default groups
 218                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 219                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 220                                         numGroups++;
 221                                         allGroups += tmap->namesOfGroups[i];
 222                                 }
 223                                 globaldata->setGroups("");
 224                         }
 225                 }else {
 226                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 227                                 allGroups += tmap->namesOfGroups[i];
 228                         }
 229                         numGroups = 1;
 230                 }
 231
 232                 //calculate number of comparsions
 233                 numComp = 0;
 234                 for (int r=0; r<numGroups; r++) {
 235                         for (int l = r+1; l < numGroups; l++) {
 236                                 groupComb.push_back(globaldata->Groups[r]+globaldata->Groups[l]);
 237                                 numComp++;
 238                         }
 239                 }
 240
 241                 //ABC
 242                 if (numComp != 1) {
 243                         groupComb.push_back(allGroups);
 244                         numComp++;
 245                 }
 246         }
 247         catch(exception& e) {
 248                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 249                 exit(1);
 250         }
 251         catch(...) {
 252                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 253                 exit(1);
 254         }
 255
 256 }
 257 /*****************************************************************/
 258
 259 void UnifracUnweightedCommand::initFile(string label){
 260         try {
 261                 if(counter != 0){
 262                         openOutputFile(unweightedFileout, out);
 263                         openInputFile(unweightedFile, inFile);
 264
 265                         string inputBuffer;
 266                         getline(inFile, inputBuffer);
 267
 268                         out     <<  inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 269                 }else{
 270                         openOutputFile(unweightedFileout, out);
 271                         out     << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 272                 }
 273
 274                 out.setf(ios::fixed, ios::floatfield);
 275                 out.setf(ios::showpoint);
 276         }
 277         catch(exception& e) {
 278                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 279                 exit(1);
 280         }
 281         catch(...) {
 282                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 283                 exit(1);
 284         }
 285 }
 286
 287 /***********************************************************************/
 288
 289 void UnifracUnweightedCommand::output(vector<double> data){
 290         try {
 291                 if(counter != 0){
 292                         string inputBuffer;
 293                         getline(inFile, inputBuffer);
 294
 295                         out     <<  inputBuffer << setprecision(6) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 296                 }
 297                 else{
 298                         out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 299                 }
 300
 301         }
 302         catch(exception& e) {
 303                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 304                 exit(1);
 305         }
 306         catch(...) {
 307                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 308                 exit(1);
 309         }
 310 };
 311
 312 /***********************************************************************/
 313
 314 void UnifracUnweightedCommand::resetFile(){
 315         try {
 316                 if(counter != 0){
 317                         out.close();
 318                         inFile.close();
 319                 }
 320                 else{
 321                         out.close();
 322                 }
 323                 counter = 1;
 324
 325                 remove(unweightedFile.c_str());
 326                 rename(unweightedFileout.c_str(), unweightedFile.c_str());
 327         }
 328         catch(exception& e) {
 329                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 330                 exit(1);
 331         }
 332         catch(...) {
 333                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 334                 exit(1);
 335         }
 336 }
 337