unifracweightedcommand.cpp

   1 /*
   2  *  unifracweightedcommand.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 "unifracweightedcommand.h"
  11
  12 /***********************************************************/
  13 UnifracWeightedCommand::UnifracWeightedCommand(string option) {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 abort = false;
  17                 Groups.clear();
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"groups","iters","distance","random","outputdir","inputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters=parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         if (globaldata->gTree.size() == 0) {//no trees were read
  38                                 mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); mothurOutEndLine(); abort = true;  }
  39
  40                         //if the user changes the output directory command factory will send this info to us in the output parameter
  41                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  42                                 outputDir = "";
  43                                 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  44                         }
  45
  46                         //check for optional parameter and set defaults
  47                         // ...at some point should added some additional type checking...
  48                         groups = validParameter.validFile(parameters, "groups", false);
  49                         if (groups == "not found") { groups = ""; }
  50                         else {
  51                                 splitAtDash(groups, Groups);
  52                                 globaldata->Groups = Groups;
  53                         }
  54
  55                         itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
  56                         convert(itersString, iters);
  57
  58                         string temp = validParameter.validFile(parameters, "distance", false);                  if (temp == "not found") { temp = "false"; }
  59                         phylip = isTrue(temp);
  60
  61                         temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "true"; }
  62                         random = isTrue(temp);
  63
  64                         if (!random) {  iters = 0;  } //turn off random calcs
  65
  66
  67                         if (abort == false) {
  68                                 T = globaldata->gTree;
  69                                 tmap = globaldata->gTreemap;
  70                                 sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary";
  71                                 openOutputFile(sumFile, outSum);
  72
  73                                 util = new SharedUtil();
  74                                 string s; //to make work with setgroups
  75                                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, s, numGroups, "weighted");     //sets the groups the user wants to analyze
  76                                 util->getCombos(groupComb, globaldata->Groups, numComp);
  77
  78                                 weighted = new Weighted(tmap);
  79
  80                         }
  81                 }
  82
  83
  84         }
  85         catch(exception& e) {
  86                 errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91
  92 void UnifracWeightedCommand::help(){
  93         try {
  94                 mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
  95                 mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random.  No parameters are required.\n");
  96                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
  97                 mothurOut("The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
  98                 mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
  99                 mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
 100                 mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
 101                 mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n");
 102                 mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
 103                 mothurOut("The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n");
 104                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 105         }
 106         catch(exception& e) {
 107                 errorOut(e, "UnifracWeightedCommand", "help");
 108                 exit(1);
 109         }
 110 }
 111
 112 /***********************************************************/
 113 int UnifracWeightedCommand::execute() {
 114         try {
 115
 116                 if (abort == true) { return 0; }
 117
 118                 Progress* reading;
 119                 if (random) {   reading = new Progress("Comparing to random:", iters);  }
 120
 121                 //get weighted for users tree
 122                 userData.resize(numComp,0);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
 123                 randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
 124
 125                 //create new tree with same num nodes and leaves as users
 126                 randT = new Tree();
 127
 128                 //get weighted scores for users trees
 129                 for (int i = 0; i < T.size(); i++) {
 130                         counter = 0;
 131                         rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
 132                         uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
 133
 134                         if (random) {  output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted", itersString);  }
 135
 136                         userData = weighted->getValues(T[i]);  //userData[0] = weightedscore
 137
 138                         //save users score
 139                         for (int s=0; s<numComp; s++) {
 140                                 //add users score to vector of user scores
 141                                 uScores[s].push_back(userData[s]);
 142
 143                                 //save users tree score for summary file
 144                                 utreeScores.push_back(userData[s]);
 145                         }
 146
 147                         //get scores for random trees
 148                         for (int j = 0; j < iters; j++) {
 149                                 int count = 0;
 150                                 for (int r=0; r<numGroups; r++) {
 151                                         for (int l = r+1; l < numGroups; l++) {
 152                                                 //copy T[i]'s info.
 153                                                 randT->getCopy(T[i]);
 154
 155                                                 //create a random tree with same topology as T[i], but different labels
 156                                                 randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
 157                                                 //get wscore of random tree
 158                                                 randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
 159
 160                                                 //save scores
 161                                                 rScores[count].push_back(randomData[0]);
 162                                                 count++;
 163                                         }
 164                                 }
 165
 166                                 //update progress bar
 167                                 reading->update(j);
 168
 169                         }
 170
 171                         //removeValidScoresDuplicates();
 172                         //find the signifigance of the score for summary file
 173                         if (random) {
 174                                 for (int f = 0; f < numComp; f++) {
 175                                         //sort random scores
 176                                         sort(rScores[f].begin(), rScores[f].end());
 177
 178                                         //the index of the score higher than yours is returned
 179                                         //so if you have 1000 random trees the index returned is 100
 180                                         //then there are 900 trees with a score greater then you.
 181                                         //giving you a signifigance of 0.900
 182                                         int index = findIndex(userData[f], f);    if (index == -1) { mothurOut("error in UnifracWeightedCommand"); mothurOutEndLine(); exit(1); } //error code
 183
 184                                         //the signifigance is the number of trees with the users score or higher
 185                                         WScoreSig.push_back((iters-index)/(float)iters);
 186                                 }
 187
 188                                 //out << "Tree# " << i << endl;
 189                                 calculateFreqsCumuls();
 190                                 printWeightedFile();
 191
 192                                 delete output;
 193                         }
 194
 195                         //clear data
 196                         rScores.clear();
 197                         uScores.clear();
 198                         validScores.clear();
 199                 }
 200
 201                 //finish progress bar
 202                 if (random) {   reading->finish();      delete reading;         }
 203
 204                 printWSummaryFile();
 205
 206                 if (phylip) {   createPhylipFile();             }
 207
 208                 //clear out users groups
 209                 globaldata->Groups.clear();
 210
 211                 delete randT;
 212
 213                 return 0;
 214
 215         }
 216         catch(exception& e) {
 217                 errorOut(e, "UnifracWeightedCommand", "execute");
 218                 exit(1);
 219         }
 220 }
 221 /***********************************************************/
 222 void UnifracWeightedCommand::printWeightedFile() {
 223         try {
 224                 vector<double> data;
 225                 vector<string> tags;
 226                 tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 227
 228                 for(int a = 0; a < numComp; a++) {
 229                         output->initFile(groupComb[a], tags);
 230                         //print each line
 231                         for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 232                                 data.push_back(it->first);  data.push_back(rScoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 233                                 output->output(data);
 234                                 data.clear();
 235                         }
 236                         output->resetFile();
 237                 }
 238         }
 239         catch(exception& e) {
 240                 errorOut(e, "UnifracWeightedCommand", "printWeightedFile");
 241                 exit(1);
 242         }
 243 }
 244
 245
 246 /***********************************************************/
 247 void UnifracWeightedCommand::printWSummaryFile() {
 248         try {
 249                 //column headers
 250                 outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
 251                 mothurOut("Tree#\tGroups\tWScore\tWSig"); mothurOutEndLine();
 252
 253                 //format output
 254                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 255
 256                 //print each line
 257                 int count = 0;
 258                 for (int i = 0; i < T.size(); i++) {
 259                         for (int j = 0; j < numComp; j++) {
 260                                 if (random) {
 261                                         if (WScoreSig[count] > (1/(float)iters)) {
 262                                                 outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
 263                                                 cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
 264                                                 mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" +  toString(WScoreSig[count])); mothurOutEndLine();
 265                                         }else{
 266                                                 outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
 267                                                 cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
 268                                                 mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" +  toString((1/float(iters)))); mothurOutEndLine();
 269                                         }
 270                                 }else{
 271                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
 272                                         cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
 273                                         mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); mothurOutEndLine();
 274                                 }
 275                                 count++;
 276                         }
 277                 }
 278                 outSum.close();
 279         }
 280         catch(exception& e) {
 281                 errorOut(e, "UnifracWeightedCommand", "printWSummaryFile");
 282                 exit(1);
 283         }
 284 }
 285 /***********************************************************/
 286 void UnifracWeightedCommand::createPhylipFile() {
 287         try {
 288                 int count = 0;
 289                 //for each tree
 290                 for (int i = 0; i < T.size(); i++) {
 291
 292                         string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
 293                         ofstream out;
 294                         openOutputFile(phylipFileName, out);
 295
 296                         //output numSeqs
 297                         out << globaldata->Groups.size() << endl;
 298
 299                         //make matrix with scores in it
 300                         vector< vector<float> > dists;  dists.resize(globaldata->Groups.size());
 301                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 302                                 dists[i].resize(globaldata->Groups.size(), 0.0);
 303                         }
 304
 305                         //flip it so you can print it
 306                         for (int r=0; r<globaldata->Groups.size(); r++) {
 307                                 for (int l = r+1; l < globaldata->Groups.size(); l++) {
 308                                         dists[r][l] = (1.0 - utreeScores[count]);
 309                                         dists[l][r] = (1.0 - utreeScores[count]);
 310                                         count++;
 311                                 }
 312                         }
 313
 314                         //output to file
 315                         for (int r=0; r<globaldata->Groups.size(); r++) {
 316                                 //output name
 317                                 string name = globaldata->Groups[r];
 318                                 if (name.length() < 10) { //pad with spaces to make compatible
 319                                         while (name.length() < 10) {  name += " ";  }
 320                                 }
 321                                 out << name << '\t';
 322
 323                                 //output distances
 324                                 for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
 325                                 out << endl;
 326                         }
 327                         out.close();
 328                 }
 329         }
 330         catch(exception& e) {
 331                 errorOut(e, "UnifracWeightedCommand", "createPhylipFile");
 332                 exit(1);
 333         }
 334 }
 335 /***********************************************************/
 336 int UnifracWeightedCommand::findIndex(float score, int index) {
 337         try{
 338                 for (int i = 0; i < rScores[index].size(); i++) {
 339                         if (rScores[index][i] >= score) {       return i;       }
 340                 }
 341                 return rScores[index].size();
 342         }
 343         catch(exception& e) {
 344                 errorOut(e, "UnifracWeightedCommand", "findIndex");
 345                 exit(1);
 346         }
 347 }
 348
 349 /***********************************************************/
 350
 351 void UnifracWeightedCommand::calculateFreqsCumuls() {
 352         try {
 353                 //clear out old tree values
 354                 rScoreFreq.clear();
 355                 rScoreFreq.resize(numComp);
 356                 rCumul.clear();
 357                 rCumul.resize(numComp);
 358                 validScores.clear();
 359
 360                 //calculate frequency
 361                 for (int f = 0; f < numComp; f++) {
 362                         for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7...  you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
 363                                 validScores[rScores[f][i]] = rScores[f][i];
 364                                 map<float,float>::iterator it = rScoreFreq[f].find(rScores[f][i]);
 365                                 if (it != rScoreFreq[f].end()) {
 366                                         rScoreFreq[f][rScores[f][i]]++;
 367                                 }else{
 368                                         rScoreFreq[f][rScores[f][i]] = 1;
 369                                 }
 370                         }
 371                 }
 372
 373                 //calculate rcumul
 374                 for(int a = 0; a < numComp; a++) {
 375                         float rcumul = 1.0000;
 376                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 377                         for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 378                                 //make rscoreFreq map and rCumul
 379                                 map<float,float>::iterator it2 = rScoreFreq[a].find(it->first);
 380                                 rCumul[a][it->first] = rcumul;
 381                                 //get percentage of random trees with that info
 382                                 if (it2 != rScoreFreq[a].end()) {  rScoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 383                                 else { rScoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 384                         }
 385                 }
 386
 387         }
 388         catch(exception& e) {
 389                 errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums");
 390                 exit(1);
 391         }
 392 }
 393
 394 /***********************************************************/
 395
 396
 397
 398
 399