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