parsimonycommand.cpp

   1 /*
   2  *  parsimonycommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/26/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "parsimonycommand.h"
  11
  12 /***********************************************************/
  13 ParsimonyCommand::ParsimonyCommand(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[] =  {"random","groups","iters","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                         randomtree = validParameter.validFile(parameters, "random", false);             if (randomtree == "not found") { randomtree = ""; }
  38
  39                         //are you trying to use parsimony without reading a tree or saying you want random distribution
  40                         if (randomtree == "")  {
  41                                 if (globaldata->gTree.size() == 0) {
  42                                         m->mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); m->mothurOutEndLine(); abort = true;  }
  43                         }
  44
  45                         //if the user changes the output directory command factory will send this info to us in the output parameter
  46                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = ""; }
  47
  48                         //check for optional parameter and set defaults
  49                         // ...at some point should added some additional type checking...
  50                         groups = validParameter.validFile(parameters, "groups", false);
  51                         if (groups == "not found") { groups = ""; globaldata->Groups.clear(); }
  52                         else {
  53                                 m->splitAtDash(groups, Groups);
  54                                 globaldata->Groups = Groups;
  55                         }
  56
  57                         itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
  58                         convert(itersString, iters);
  59
  60                         if (abort == false) {
  61                                 //randomtree will tell us if user had their own treefile or if they just want the random distribution
  62                                 //user has entered their own tree
  63                                 if (randomtree == "") {
  64                                         T = globaldata->gTree;
  65                                         tmap = globaldata->gTreemap;
  66
  67                                         if(outputDir == "") { outputDir += m->hasPath(globaldata->getTreeFile()); }
  68                                         output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  +  ".parsimony", itersString);
  69                                         outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  +  ".parsimony");
  70
  71                                         sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".psummary";
  72                                         m->openOutputFile(sumFile, outSum);
  73                                         outputNames.push_back(sumFile);
  74                                 }else { //user wants random distribution
  75                                         savetmap = globaldata->gTreemap;
  76                                         getUserInput();
  77
  78                                         if(outputDir == "") { outputDir += m->hasPath(randomtree); }
  79                                         output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
  80                                         outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
  81                                 }
  82
  83                                 //set users groups to analyze
  84                                 util = new SharedUtil();
  85                                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");    //sets the groups the user wants to analyze
  86                                 util->getCombos(groupComb, globaldata->Groups, numComp);
  87
  88                                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
  89
  90                                 pars = new Parsimony(tmap);
  91                                 counter = 0;
  92
  93                         }
  94
  95                 }
  96
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
 100                 exit(1);
 101         }
 102 }
 103
 104 //**********************************************************************************************************************
 105
 106 void ParsimonyCommand::help(){
 107         try {
 108                 m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
 109                 m->mothurOut("The parsimony command parameters are random, groups and iters.  No parameters are required.\n");
 110                 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 1 valid group.\n");
 111                 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");
 112                 m->mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
 113                 m->mothurOut("Example parsimony(random=out, iters=500).\n");
 114                 m->mothurOut("The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n");
 115                 m->mothurOut("and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
 116                 m->mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n");
 117         }
 118         catch(exception& e) {
 119                 m->errorOut(e, "ParsimonyCommand", "help");
 120                 exit(1);
 121         }
 122 }
 123
 124
 125 /***********************************************************/
 126 int ParsimonyCommand::execute() {
 127         try {
 128
 129                 if (abort == true) { return 0; }
 130
 131                 Progress* reading;
 132                 reading = new Progress("Comparing to random:", iters);
 133
 134                 if (m->control_pressed) {
 135                         delete reading; delete pars; delete util; delete output;
 136                         if (randomtree == "") {  outSum.close();  }
 137                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 138                         globaldata->Groups.clear();
 139                         return 0;
 140                 }
 141
 142
 143                 //get pscore for users tree
 144                 userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 145                 randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 146                 rscoreFreq.resize(numComp);
 147                 uscoreFreq.resize(numComp);
 148                 rCumul.resize(numComp);
 149                 uCumul.resize(numComp);
 150                 userTreeScores.resize(numComp);
 151                 UScoreSig.resize(numComp);
 152
 153                 if (randomtree == "") {
 154                         //get pscores for users trees
 155                         for (int i = 0; i < T.size(); i++) {
 156                                 userData = pars->getValues(T[i]);  //data = AB, AC, BC, ABC.
 157
 158                                 if (m->control_pressed) {
 159                                         delete reading; delete pars; delete util; delete output;
 160                                         if (randomtree == "") {  outSum.close();  }
 161                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 162                                         globaldata->Groups.clear();
 163                                         return 0;
 164                                 }
 165
 166
 167                                 //output scores for each combination
 168                                 for(int k = 0; k < numComp; k++) {
 169
 170                                         //update uscoreFreq
 171                                         map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
 172                                         if (it == uscoreFreq[k].end()) {//new score
 173                                                 uscoreFreq[k][userData[k]] = 1;
 174                                         }else{ uscoreFreq[k][userData[k]]++; }
 175
 176                                         //add users score to valid scores
 177                                         validScores[userData[k]] = userData[k];
 178
 179                                         //save score for summary file
 180                                         userTreeScores[k].push_back(userData[k]);
 181                                 }
 182                         }
 183
 184                         //get pscores for random trees
 185                         for (int j = 0; j < iters; j++) {
 186
 187                                 //create new tree with same num nodes and leaves as users
 188                                 randT = new Tree();
 189
 190                                 //create random relationships between nodes
 191                                 randT->assembleRandomTree();
 192
 193                                 //get pscore of random tree
 194                                 randomData = pars->getValues(randT);
 195
 196                                 if (m->control_pressed) {
 197                                         delete reading; delete pars; delete util; delete output; delete randT;
 198                                         if (randomtree == "") {  outSum.close();  }
 199                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 200                                         globaldata->Groups.clear();
 201                                         return 0;
 202                                 }
 203
 204                                 for(int r = 0; r < numComp; r++) {
 205                                         //add trees pscore to map of scores
 206                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 207                                         if (it != rscoreFreq[r].end()) {//already have that score
 208                                                 rscoreFreq[r][randomData[r]]++;
 209                                         }else{//first time we have seen this score
 210                                                 rscoreFreq[r][randomData[r]] = 1;
 211                                         }
 212
 213                                         //add randoms score to validscores
 214                                         validScores[randomData[r]] = randomData[r];
 215                                 }
 216
 217                                 //update progress bar
 218                                 reading->update(j);
 219
 220                                 delete randT;
 221                         }
 222
 223                 }else {
 224                         //get pscores for random trees
 225                         for (int j = 0; j < iters; j++) {
 226
 227                                 //create new tree with same num nodes and leaves as users
 228                                 randT = new Tree();
 229                                 //create random relationships between nodes
 230
 231                                 randT->assembleRandomTree();
 232
 233                                 if (m->control_pressed) {
 234                                         delete reading; delete pars; delete util; delete output; delete randT;
 235                                         globaldata->gTreemap = savetmap;
 236                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 237                                         globaldata->Groups.clear();
 238                                         return 0;
 239                                 }
 240
 241
 242                                 //get pscore of random tree
 243                                 randomData = pars->getValues(randT);
 244
 245                                 if (m->control_pressed) {
 246                                         delete reading; delete pars; delete util; delete output; delete randT;
 247                                         globaldata->gTreemap = savetmap;
 248                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 249                                         globaldata->Groups.clear();
 250                                         return 0;
 251                                 }
 252
 253                                 for(int r = 0; r < numComp; r++) {
 254                                         //add trees pscore to map of scores
 255                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 256                                         if (it != rscoreFreq[r].end()) {//already have that score
 257                                                 rscoreFreq[r][randomData[r]]++;
 258                                         }else{//first time we have seen this score
 259                                                 rscoreFreq[r][randomData[r]] = 1;
 260                                         }
 261
 262                                         //add randoms score to validscores
 263                                         validScores[randomData[r]] = randomData[r];
 264                                 }
 265
 266                                 //update progress bar
 267                                 reading->update(j);
 268
 269                                 delete randT;
 270                         }
 271                 }
 272
 273                 for(int a = 0; a < numComp; a++) {
 274                         float rcumul = 0.0000;
 275                         float ucumul = 0.0000;
 276                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 277                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 278                                 if (randomtree == "") {
 279                                         map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
 280                                         //user data has that score
 281                                         if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
 282                                         else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
 283                                         //make uCumul map
 284                                         uCumul[a][it->first] = ucumul;
 285                                 }
 286
 287                                 //make rscoreFreq map and rCumul
 288                                 map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
 289                                 //get percentage of random trees with that info
 290                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
 291                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 292                                 rCumul[a][it->first] = rcumul;
 293                         }
 294
 295                         //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 296                         for (int h = 0; h < userTreeScores[a].size(); h++) {
 297                                 UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
 298                         }
 299                 }
 300
 301                 if (m->control_pressed) {
 302                                 delete reading; delete pars; delete util; delete output;
 303                                 if (randomtree == "") {  outSum.close();  }
 304                                 else { globaldata->gTreemap = savetmap; }
 305                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 306                                 globaldata->Groups.clear();
 307                                 return 0;
 308                 }
 309
 310                 //finish progress bar
 311                 reading->finish();
 312                 delete reading;
 313
 314
 315                 printParsimonyFile();
 316                 if (randomtree == "") { printUSummaryFile(); }
 317
 318                 //reset globaldata's treemap if you just did random distrib
 319                 if (randomtree != "") {
 320                         //memory leak prevention
 321                         //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
 322                         globaldata->gTreemap = savetmap;
 323                 }
 324
 325                 //reset groups parameter
 326                 globaldata->Groups.clear();
 327
 328                 if (m->control_pressed) {
 329                         delete pars; delete util; delete output;
 330                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 331                         return 0;
 332                 }
 333
 334                 m->mothurOutEndLine();
 335                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 336                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 337                 m->mothurOutEndLine();
 338
 339
 340                 return 0;
 341
 342         }
 343         catch(exception& e) {
 344                 m->errorOut(e, "ParsimonyCommand", "execute");
 345                 exit(1);
 346         }
 347 }
 348
 349 /***********************************************************/
 350 void ParsimonyCommand::printParsimonyFile() {
 351         try {
 352                 vector<double> data;
 353                 vector<string> tags;
 354
 355                 if (randomtree == "") {
 356                         tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 357                 }else {
 358                         tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 359                 }
 360
 361                 for(int a = 0; a < numComp; a++) {
 362                         output->initFile(groupComb[a], tags);
 363                         //print each line
 364                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 365                                 if (randomtree == "") {
 366                                         data.push_back(it->first);  data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 367                                 }else{
 368                                         data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 369                                 }
 370                                 output->output(data);
 371                                 data.clear();
 372                         }
 373                         output->resetFile();
 374                 }
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
 378                 exit(1);
 379         }
 380 }
 381 /***********************************************************/
 382 int ParsimonyCommand::printUSummaryFile() {
 383         try {
 384                 //column headers
 385                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 386                 m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
 387
 388                 //format output
 389                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 390
 391
 392                 //print each line
 393                 for (int i = 0; i< T.size(); i++) {
 394                         for(int a = 0; a < numComp; a++) {
 395                                 if (m->control_pressed) {  outSum.close(); return 0; }
 396                                 if (UScoreSig[a][i] > (1/(float)iters)) {
 397                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 398                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 399                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
 400                                 }else {
 401                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length())  << '\t' << "<" << (1/float(iters)) << endl;
 402                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
 403                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
 404                                 }
 405                         }
 406                 }
 407
 408                 outSum.close();
 409                 return 0;
 410         }
 411         catch(exception& e) {
 412                 m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
 413                 exit(1);
 414         }
 415 }
 416
 417 /***********************************************************/
 418 void ParsimonyCommand::getUserInput() {
 419         try {
 420
 421                 //create treemap
 422                 tmap = new TreeMap();
 423
 424                 m->mothurOut("Please enter the number of groups you would like to analyze: ");
 425                 cin >> numGroups;
 426                 m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
 427
 428                 int num, count;
 429                 count = 1;
 430                 numEachGroup.resize(numGroups, 0);
 431
 432                 for (int i = 1; i <= numGroups; i++) {
 433                         m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
 434                         cin >> num;
 435                         m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
 436
 437                         //set tmaps seqsPerGroup
 438                         tmap->seqsPerGroup[toString(i)] = num;
 439                         tmap->namesOfGroups.push_back(toString(i));
 440
 441                         //set tmaps namesOfSeqs
 442                         for (int j = 0; j < num; j++) {
 443                                 tmap->namesOfSeqs.push_back(toString(count));
 444                                 tmap->treemap[toString(count)].groupname = toString(i);
 445                                 count++;
 446                         }
 447                 }
 448
 449                 //clears buffer so next command doesn't have error
 450                 string s;
 451                 getline(cin, s);
 452
 453                 //save tmap for later
 454                 //memory leak prevention
 455                 //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
 456                 globaldata->gTreemap = tmap;
 457                 globaldata->Treenames = tmap->namesOfSeqs;
 458
 459         }
 460         catch(exception& e) {
 461                 m->errorOut(e, "ParsimonyCommand", "getUserInput");
 462                 exit(1);
 463         }
 464 }
 465
 466 /***********************************************************/
 467
 468