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