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                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
  45                 cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" << '\t' << "UWSig" <<  endl;
  46
  47                 //get pscores for users trees
  48                 for (int i = 0; i < T.size(); i++) {
  49                         counter = 0;
  50                         unweightedFile = globaldata->getTreeFile()  + toString(i+1) + ".unweighted";
  51                         unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
  52
  53                         outSum << i+1 << '\t';
  54                         cout << i+1 << '\t';
  55
  56                         //get unweighted for users tree
  57                         rscoreFreq.resize(numComp);
  58                         rCumul.resize(numComp);
  59                         utreeScores.resize(numComp);
  60                         UWScoreSig.resize(numComp);
  61
  62                         userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
  63
  64                         //output scores for each combination
  65                         for(int k = 0; k < numComp; k++) {
  66                                 //saves users score
  67                                 utreeScores[k].push_back(userData[k]);
  68
  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                                         //add trees unweighted score to map of scores
  78                                         it2 = rscoreFreq[k].find(randomData[k]);
  79                                         if (it2 != rscoreFreq[k].end()) {//already have that score
  80                                                 rscoreFreq[k][randomData[k]]++;
  81                                         }else{//first time we have seen this score
  82                                                 rscoreFreq[k][randomData[k]] = 1;
  83                                         }
  84
  85                                         //add randoms score to validscores
  86                                         validScores[randomData[k]] = randomData[k];
  87                                 }
  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.begin(); it != validScores.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
 106
 107                 printUnweightedFile();
 108                 printUWSummaryFile();
 109
 110                 rscoreFreq.clear();
 111                 rCumul.clear();
 112                 validScores.clear();
 113                 utreeScores.clear();
 114                 UWScoreSig.clear();
 115         }
 116                 //reset groups parameter
 117                 globaldata->Groups.clear(); globaldata->setGroups("");
 118                 outSum.close();
 119
 120                 return 0;
 121
 122         }
 123         catch(exception& e) {
 124                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 125                 exit(1);
 126         }
 127         catch(...) {
 128                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 129                 exit(1);
 130         }
 131 }
 132 /***********************************************************/
 133 void UnifracUnweightedCommand::printUnweightedFile() {
 134         try {
 135                 vector<double> data;
 136
 137                 for(int a = 0; a < numComp; a++) {
 138                         initFile(groupComb[a]);
 139                         //print each line
 140                         for (it = validScores.begin(); it != validScores.end(); it++) {
 141                                 data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 142                                 output(data);
 143                                 data.clear();
 144                         }
 145                         resetFile();
 146                 }
 147
 148                 out.close();
 149                 inFile.close();
 150                 remove(unweightedFileout.c_str());
 151
 152         }
 153         catch(exception& e) {
 154                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 155                 exit(1);
 156         }
 157         catch(...) {
 158                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 159                 exit(1);
 160         }
 161 }
 162
 163 /***********************************************************/
 164 void UnifracUnweightedCommand::printUWSummaryFile() {
 165         try {
 166
 167                 //format output
 168                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 169
 170                 //print each line
 171
 172                 for(int a = 0; a < numComp; a++) {
 173                         if (UWScoreSig[a][0] > (1/(float)iters)) {
 174                                 outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
 175                                 cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
 176                         }else {
 177                                 outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
 178                                 cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
 179                         }
 180                 }
 181
 182         }
 183         catch(exception& e) {
 184                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 185                 exit(1);
 186         }
 187         catch(...) {
 188                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 189                 exit(1);
 190         }
 191 }
 192 /***********************************************************/
 193
 194 void UnifracUnweightedCommand::setGroups() {
 195         try {
 196                 string allGroups = "";
 197                 numGroups = 0;
 198                 //if the user has not entered specific groups to analyze then do them all
 199                 if (globaldata->Groups.size() != 0) {
 200                         if (globaldata->Groups[0] != "all") {
 201                                 //check that groups are valid
 202                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 203                                         if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 204                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 205                                                 // erase the invalid group from globaldata->Groups
 206                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 207                                         }
 208                                 }
 209
 210                                 //if the user only entered invalid groups
 211                                 if (globaldata->Groups.size() == 0) {
 212                                         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;
 213                                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 214                                                 if (tmap->namesOfGroups[i] != "xxx") {
 215                                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 216                                                         numGroups++;
 217                                                         allGroups += tmap->namesOfGroups[i] + "-";
 218                                                 }
 219                                         }
 220                                         allGroups = allGroups.substr(0, allGroups.length()-1);
 221                                 }else {
 222                                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 223                                                 allGroups += globaldata->Groups[i] + "-";
 224                                                 numGroups++;
 225                                         }
 226                                         allGroups = allGroups.substr(0, allGroups.length()-1);
 227                                 }
 228                         }else{//user has enter "all" and wants the default groups
 229                                 globaldata->Groups.clear();
 230                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 231                                         if (tmap->namesOfGroups[i] != "xxx") {
 232                                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 233                                                 numGroups++;
 234                                                 allGroups += tmap->namesOfGroups[i] + "-";
 235                                         }
 236                                 }
 237                                 allGroups = allGroups.substr(0, allGroups.length()-1);
 238                                 globaldata->setGroups("");
 239                         }
 240                 }else {
 241                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 242                                 if (tmap->namesOfGroups[i] != "xxx") {
 243                                         allGroups += tmap->namesOfGroups[i] + "-";
 244                                 }
 245                         }
 246                         allGroups = allGroups.substr(0, allGroups.length()-1);
 247                         numGroups = 1;
 248                 }
 249
 250                 //calculate number of comparsions
 251                 numComp = 0;
 252                 for (int r=0; r<numGroups; r++) {
 253                         for (int l = r+1; l < numGroups; l++) {
 254                                 groupComb.push_back(globaldata->Groups[r]+ "-" + globaldata->Groups[l]);
 255                                 numComp++;
 256                         }
 257                 }
 258
 259                 //ABC
 260                 if (numComp != 1) {
 261                         groupComb.push_back(allGroups);
 262                         numComp++;
 263                 }
 264         }
 265         catch(exception& e) {
 266                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 267                 exit(1);
 268         }
 269         catch(...) {
 270                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 271                 exit(1);
 272         }
 273
 274 }
 275 /*****************************************************************/
 276
 277 void UnifracUnweightedCommand::initFile(string label){
 278         try {
 279                 if(counter != 0){
 280                         openOutputFile(unweightedFileout, out);
 281                         openInputFile(unweightedFile, inFile);
 282
 283                         string inputBuffer;
 284                         getline(inFile, inputBuffer);
 285
 286                         out     <<  inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 287                 }else{
 288                         openOutputFile(unweightedFileout, out);
 289                         out     << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 290                 }
 291
 292                 out.setf(ios::fixed, ios::floatfield);
 293                 out.setf(ios::showpoint);
 294         }
 295         catch(exception& e) {
 296                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 297                 exit(1);
 298         }
 299         catch(...) {
 300                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 301                 exit(1);
 302         }
 303 }
 304
 305 /***********************************************************************/
 306
 307 void UnifracUnweightedCommand::output(vector<double> data){
 308         try {
 309                 if(counter != 0){
 310                         string inputBuffer;
 311                         getline(inFile, inputBuffer);
 312 //                      out     <<  inputBuffer << setprecision(6) << '\t' << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
 313
 314                         out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 315                 }
 316                 else{
 317                         out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 318                 }
 319
 320         }
 321         catch(exception& e) {
 322                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 323                 exit(1);
 324         }
 325         catch(...) {
 326                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 327                 exit(1);
 328         }
 329 };
 330
 331 /***********************************************************************/
 332
 333 void UnifracUnweightedCommand::resetFile(){
 334         try {
 335                 if(counter != 0){
 336                         out.close();
 337                         inFile.close();
 338                 }
 339                 else{
 340                         out.close();
 341                 }
 342                 counter = 1;
 343
 344                 remove(unweightedFile.c_str());
 345                 rename(unweightedFileout.c_str(), unweightedFile.c_str());
 346         }
 347         catch(exception& e) {
 348                 cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 349                 exit(1);
 350         }
 351         catch(...) {
 352                 cout << "An unknown error has occurred in the UnifracUnweightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 353                 exit(1);
 354         }
 355 }
 356