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","processors","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                                 m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->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 += m->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                                 m->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 = m->isTrue(temp);
  60
  61                         temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "F"; }
  62                         random = m->isTrue(temp);
  63
  64                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
  65                         convert(temp, processors);
  66
  67                         if (!random) {  iters = 0;  } //turn off random calcs
  68
  69
  70                         if (abort == false) {
  71                                 T = globaldata->gTree;
  72                                 tmap = globaldata->gTreemap;
  73                                 sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary";
  74                                 m->openOutputFile(sumFile, outSum);
  75                                 outputNames.push_back(sumFile);
  76
  77                                 util = new SharedUtil();
  78                                 string s; //to make work with setgroups
  79                                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, s, numGroups, "weighted");     //sets the groups the user wants to analyze
  80                                 util->getCombos(groupComb, globaldata->Groups, numComp);
  81
  82                                 weighted = new Weighted(tmap);
  83
  84                         }
  85                 }
  86
  87
  88         }
  89         catch(exception& e) {
  90                 m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
  91                 exit(1);
  92         }
  93 }
  94 //**********************************************************************************************************************
  95
  96 void UnifracWeightedCommand::help(){
  97         try {
  98                 m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
  99                 m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance, processors and random.  No parameters are required.\n");
 100                 m->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");
 101                 m->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");
 102                 m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
 103                 m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n");
 104                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 105                 m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
 106                 m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n");
 107                 m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
 108                 m->mothurOut("The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n");
 109                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 110         }
 111         catch(exception& e) {
 112                 m->errorOut(e, "UnifracWeightedCommand", "help");
 113                 exit(1);
 114         }
 115 }
 116
 117 /***********************************************************/
 118 int UnifracWeightedCommand::execute() {
 119         try {
 120
 121                 if (abort == true) { return 0; }
 122
 123                 int start = time(NULL);
 124
 125                 //get weighted for users tree
 126                 userData.resize(numComp,0);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
 127                 randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
 128
 129                 //get weighted scores for users trees
 130                 for (int i = 0; i < T.size(); i++) {
 131
 132                         if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 133
 134                         counter = 0;
 135                         rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
 136                         uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
 137
 138                         if (random) {
 139                                 output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted", itersString);
 140                                 outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted");
 141                         }
 142
 143                         userData = weighted->getValues(T[i], processors, outputDir);  //userData[0] = weightedscore
 144
 145                         if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());  } return 0; }
 146
 147                         //save users score
 148                         for (int s=0; s<numComp; s++) {
 149                                 //add users score to vector of user scores
 150                                 uScores[s].push_back(userData[s]);
 151
 152                                 //save users tree score for summary file
 153                                 utreeScores.push_back(userData[s]);
 154                         }
 155
 156                         if (random) {
 157                                 vector<double> sums = weighted->getBranchLengthSums(T[i]);
 158
 159                                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 160                                 vector< vector<string> > namesOfGroupCombos;
 161                                 for (int a=0; a<numGroups; a++) {
 162                                         for (int l = 0; l < a; l++) {
 163                                                 vector<string> groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 164                                                 namesOfGroupCombos.push_back(groups);
 165                                         }
 166                                 }
 167
 168                                 lines.clear();
 169
 170                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 171                                         if(processors != 1){
 172                                                 int numPairs = namesOfGroupCombos.size();
 173                                                 int numPairsPerProcessor = numPairs / processors;
 174
 175                                                 for (int i = 0; i < processors; i++) {
 176                                                         int startPos = i * numPairsPerProcessor;
 177                                                         if(i == processors - 1){
 178                                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
 179                                                         }
 180                                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
 181                                                 }
 182                                         }
 183                                 #endif
 184
 185
 186                                 //get scores for random trees
 187                                 for (int j = 0; j < iters; j++) {
 188
 189                                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 190                                                 if(processors == 1){
 191                                                         driver(T[i],  namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
 192                                                 }else{
 193                                                         createProcesses(T[i],  namesOfGroupCombos, sums, rScores);
 194                                                 }
 195                                         #else
 196                                                 driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
 197                                         #endif
 198
 199                                         if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());  } return 0; }
 200
 201                                         //report progress
 202                                         m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
 203                                 }
 204                                 lines.clear();
 205
 206                                 //find the signifigance of the score for summary file
 207                                 for (int f = 0; f < numComp; f++) {
 208                                         //sort random scores
 209                                         sort(rScores[f].begin(), rScores[f].end());
 210
 211                                         //the index of the score higher than yours is returned
 212                                         //so if you have 1000 random trees the index returned is 100
 213                                         //then there are 900 trees with a score greater then you.
 214                                         //giving you a signifigance of 0.900
 215                                         int index = findIndex(userData[f], f);    if (index == -1) { m->mothurOut("error in UnifracWeightedCommand"); m->mothurOutEndLine(); exit(1); } //error code
 216
 217                                         //the signifigance is the number of trees with the users score or higher
 218                                         WScoreSig.push_back((iters-index)/(float)iters);
 219                                 }
 220
 221                                 //out << "Tree# " << i << endl;
 222                                 calculateFreqsCumuls();
 223                                 printWeightedFile();
 224
 225                                 delete output;
 226
 227                         }
 228
 229                         //clear data
 230                         rScores.clear();
 231                         uScores.clear();
 232                         validScores.clear();
 233                 }
 234
 235
 236                 if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0;  }
 237
 238                 printWSummaryFile();
 239
 240                 if (phylip) {   createPhylipFile();             }
 241
 242                 //clear out users groups
 243                 globaldata->Groups.clear();
 244
 245
 246                 if (m->control_pressed) {
 247                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 248                         return 0;
 249                 }
 250
 251                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.weighted."); m->mothurOutEndLine();
 252
 253                 m->mothurOutEndLine();
 254                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 255                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 256                 m->mothurOutEndLine();
 257
 258                 return 0;
 259
 260         }
 261         catch(exception& e) {
 262                 m->errorOut(e, "UnifracWeightedCommand", "execute");
 263                 exit(1);
 264         }
 265 }
 266 /**************************************************************************************************/
 267
 268 int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
 269         try {
 270 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 271                 int process = 1;
 272                 int num = 0;
 273                 vector<int> processIDS;
 274
 275                 EstOutput results;
 276
 277                 //loop through and create all the processes you want
 278                 while (process != processors) {
 279                         int pid = fork();
 280
 281                         if (pid > 0) {
 282                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 283                                 process++;
 284                         }else if (pid == 0){
 285                                 driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores);
 286
 287                                 //pass numSeqs to parent
 288                                 ofstream out;
 289                                 string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
 290                                 m->openOutputFile(tempFile, out);
 291                                 for (int i = lines[process].start; i < (lines[process].start + lines[process].num); i++) { out << scores[i][(scores[i].size()-1)] << '\t';  } out << endl;
 292                                 out.close();
 293
 294                                 exit(0);
 295                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 296                 }
 297
 298                 driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums, scores);
 299
 300                 //force parent to wait until all the processes are done
 301                 for (int i=0;i<(processors-1);i++) {
 302                         int temp = processIDS[i];
 303                         wait(&temp);
 304                 }
 305
 306                 //get data created by processes
 307                 for (int i=0;i<(processors-1);i++) {
 308
 309                         ifstream in;
 310                         string s = outputDir + toString(processIDS[i]) + ".weightedcommand.results.temp";
 311                         m->openInputFile(s, in);
 312
 313                         double tempScore;
 314                         for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
 315                         in.close();
 316                         remove(s.c_str());
 317                 }
 318
 319                 return 0;
 320 #endif
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "UnifracWeightedCommand", "createProcesses");
 324                 exit(1);
 325         }
 326 }
 327
 328 /**************************************************************************************************/
 329 int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
 330  try {
 331                 Tree* randT = new Tree();
 332
 333                 for (int h = start; h < (start+num); h++) {
 334
 335                         if (m->control_pressed) { return 0; }
 336
 337                         //initialize weighted score
 338                         string groupA = namesOfGroupCombos[h][0];
 339                         string groupB = namesOfGroupCombos[h][1];
 340
 341                         //copy T[i]'s info.
 342                         randT->getCopy(t);
 343
 344                         //create a random tree with same topology as T[i], but different labels
 345                         randT->assembleRandomUnifracTree(groupA, groupB);
 346
 347                         if (m->control_pressed) { delete randT;  return 0;  }
 348
 349                         //get wscore of random tree
 350                         EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums);
 351
 352                         if (m->control_pressed) { delete randT;  return 0;  }
 353
 354                         //save scores
 355                         scores[h].push_back(randomData[0]);
 356                 }
 357
 358                 delete randT;
 359
 360                 return 0;
 361
 362         }
 363         catch(exception& e) {
 364                 m->errorOut(e, "UnifracWeightedCommand", "driver");
 365                 exit(1);
 366         }
 367 }
 368 /***********************************************************/
 369 void UnifracWeightedCommand::printWeightedFile() {
 370         try {
 371                 vector<double> data;
 372                 vector<string> tags;
 373                 tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 374
 375                 for(int a = 0; a < numComp; a++) {
 376                         output->initFile(groupComb[a], tags);
 377                         //print each line
 378                         for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 379                                 data.push_back(it->first);  data.push_back(rScoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 380                                 output->output(data);
 381                                 data.clear();
 382                         }
 383                         output->resetFile();
 384                 }
 385         }
 386         catch(exception& e) {
 387                 m->errorOut(e, "UnifracWeightedCommand", "printWeightedFile");
 388                 exit(1);
 389         }
 390 }
 391
 392
 393 /***********************************************************/
 394 void UnifracWeightedCommand::printWSummaryFile() {
 395         try {
 396                 //column headers
 397                 outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
 398                 m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine();
 399
 400                 //format output
 401                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 402
 403                 //print each line
 404                 int count = 0;
 405                 for (int i = 0; i < T.size(); i++) {
 406                         for (int j = 0; j < numComp; j++) {
 407                                 if (random) {
 408                                         if (WScoreSig[count] > (1/(float)iters)) {
 409                                                 outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
 410                                                 cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
 411                                                 m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" +  toString(WScoreSig[count]) + "\n");
 412                                         }else{
 413                                                 outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
 414                                                 cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
 415                                                 m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" +  toString((1/float(iters))) + "\n");
 416                                         }
 417                                 }else{
 418                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
 419                                         cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
 420                                         m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n");
 421                                 }
 422                                 count++;
 423                         }
 424                 }
 425                 outSum.close();
 426         }
 427         catch(exception& e) {
 428                 m->errorOut(e, "UnifracWeightedCommand", "printWSummaryFile");
 429                 exit(1);
 430         }
 431 }
 432 /***********************************************************/
 433 void UnifracWeightedCommand::createPhylipFile() {
 434         try {
 435                 int count = 0;
 436                 //for each tree
 437                 for (int i = 0; i < T.size(); i++) {
 438
 439                         string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
 440                         outputNames.push_back(phylipFileName);
 441                         ofstream out;
 442                         m->openOutputFile(phylipFileName, out);
 443
 444                         //output numSeqs
 445                         out << globaldata->Groups.size() << endl;
 446
 447                         //make matrix with scores in it
 448                         vector< vector<float> > dists;  dists.resize(globaldata->Groups.size());
 449                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 450                                 dists[i].resize(globaldata->Groups.size(), 0.0);
 451                         }
 452
 453                         //flip it so you can print it
 454                         for (int r=0; r<globaldata->Groups.size(); r++) {
 455                                 for (int l = r+1; l < globaldata->Groups.size(); l++) {
 456                                         dists[r][l] = utreeScores[count];
 457                                         dists[l][r] = utreeScores[count];
 458                                         count++;
 459                                 }
 460                         }
 461
 462                         //output to file
 463                         for (int r=0; r<globaldata->Groups.size(); r++) {
 464                                 //output name
 465                                 string name = globaldata->Groups[r];
 466                                 if (name.length() < 10) { //pad with spaces to make compatible
 467                                         while (name.length() < 10) {  name += " ";  }
 468                                 }
 469                                 out << name << '\t';
 470
 471                                 //output distances
 472                                 for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
 473                                 out << endl;
 474                         }
 475                         out.close();
 476                 }
 477         }
 478         catch(exception& e) {
 479                 m->errorOut(e, "UnifracWeightedCommand", "createPhylipFile");
 480                 exit(1);
 481         }
 482 }
 483 /***********************************************************/
 484 int UnifracWeightedCommand::findIndex(float score, int index) {
 485         try{
 486                 for (int i = 0; i < rScores[index].size(); i++) {
 487                         if (rScores[index][i] >= score) {       return i;       }
 488                 }
 489                 return rScores[index].size();
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "UnifracWeightedCommand", "findIndex");
 493                 exit(1);
 494         }
 495 }
 496
 497 /***********************************************************/
 498
 499 void UnifracWeightedCommand::calculateFreqsCumuls() {
 500         try {
 501                 //clear out old tree values
 502                 rScoreFreq.clear();
 503                 rScoreFreq.resize(numComp);
 504                 rCumul.clear();
 505                 rCumul.resize(numComp);
 506                 validScores.clear();
 507
 508                 //calculate frequency
 509                 for (int f = 0; f < numComp; f++) {
 510                         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...
 511                                 validScores[rScores[f][i]] = rScores[f][i];
 512                                 map<float,float>::iterator it = rScoreFreq[f].find(rScores[f][i]);
 513                                 if (it != rScoreFreq[f].end()) {
 514                                         rScoreFreq[f][rScores[f][i]]++;
 515                                 }else{
 516                                         rScoreFreq[f][rScores[f][i]] = 1;
 517                                 }
 518                         }
 519                 }
 520
 521                 //calculate rcumul
 522                 for(int a = 0; a < numComp; a++) {
 523                         float rcumul = 1.0000;
 524                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 525                         for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 526                                 //make rscoreFreq map and rCumul
 527                                 map<float,float>::iterator it2 = rScoreFreq[a].find(it->first);
 528                                 rCumul[a][it->first] = rcumul;
 529                                 //get percentage of random trees with that info
 530                                 if (it2 != rScoreFreq[a].end()) {  rScoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 531                                 else { rScoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 532                         }
 533                 }
 534
 535         }
 536         catch(exception& e) {
 537                 m->errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums");
 538                 exit(1);
 539         }
 540 }
 541
 542 /***********************************************************/
 543
 544
 545
 546
 547