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                                         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."); 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                                 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 += hasPath(globaldata->getTreeFile()); }
  68                                         output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  +  ".parsimony", itersString);
  69
  70                                         sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary";
  71                                         openOutputFile(sumFile, outSum);
  72                                 }else { //user wants random distribution
  73                                         savetmap = globaldata->gTreemap;
  74                                         getUserInput();
  75
  76                                         if(outputDir == "") { outputDir += hasPath(randomtree); }
  77                                         output = new ColumnFile(outputDir+ getSimpleName(randomtree), itersString);
  78                                 }
  79
  80                                 //set users groups to analyze
  81                                 util = new SharedUtil();
  82                                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");    //sets the groups the user wants to analyze
  83                                 util->getCombos(groupComb, globaldata->Groups, numComp);
  84
  85                                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
  86
  87                                 pars = new Parsimony(tmap);
  88                                 counter = 0;
  89
  90                         }
  91
  92                 }
  93
  94         }
  95         catch(exception& e) {
  96                 errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
  97                 exit(1);
  98         }
  99 }
 100
 101 //**********************************************************************************************************************
 102
 103 void ParsimonyCommand::help(){
 104         try {
 105                 mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
 106                 mothurOut("The parsimony command parameters are random, groups and iters.  No parameters are required.\n");
 107                 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");
 108                 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");
 109                 mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
 110                 mothurOut("Example parsimony(random=out, iters=500).\n");
 111                 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");
 112                 mothurOut("and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
 113                 mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n");
 114         }
 115         catch(exception& e) {
 116                 errorOut(e, "ParsimonyCommand", "help");
 117                 exit(1);
 118         }
 119 }
 120
 121
 122 /***********************************************************/
 123 int ParsimonyCommand::execute() {
 124         try {
 125
 126                 if (abort == true) { return 0; }
 127
 128                 Progress* reading;
 129                 reading = new Progress("Comparing to random:", iters);
 130
 131                 //get pscore for users tree
 132                 userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 133                 randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 134                 rscoreFreq.resize(numComp);
 135                 uscoreFreq.resize(numComp);
 136                 rCumul.resize(numComp);
 137                 uCumul.resize(numComp);
 138                 userTreeScores.resize(numComp);
 139                 UScoreSig.resize(numComp);
 140
 141                 if (randomtree == "") {
 142                         //get pscores for users trees
 143                         for (int i = 0; i < T.size(); i++) {
 144                                 userData = pars->getValues(T[i]);  //data = AB, AC, BC, ABC.
 145
 146                                 //output scores for each combination
 147                                 for(int k = 0; k < numComp; k++) {
 148
 149                                         //update uscoreFreq
 150                                         map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
 151                                         if (it == uscoreFreq[k].end()) {//new score
 152                                                 uscoreFreq[k][userData[k]] = 1;
 153                                         }else{ uscoreFreq[k][userData[k]]++; }
 154
 155                                         //add users score to valid scores
 156                                         validScores[userData[k]] = userData[k];
 157
 158                                         //save score for summary file
 159                                         userTreeScores[k].push_back(userData[k]);
 160                                 }
 161                         }
 162
 163                         //get pscores for random trees
 164                         for (int j = 0; j < iters; j++) {
 165                                 //create new tree with same num nodes and leaves as users
 166                                 randT = new Tree();
 167
 168                                 //create random relationships between nodes
 169                                 randT->assembleRandomTree();
 170
 171                                 //get pscore of random tree
 172                                 randomData = pars->getValues(randT);
 173
 174                                 for(int r = 0; r < numComp; r++) {
 175                                         //add trees pscore to map of scores
 176                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 177                                         if (it != rscoreFreq[r].end()) {//already have that score
 178                                                 rscoreFreq[r][randomData[r]]++;
 179                                         }else{//first time we have seen this score
 180                                                 rscoreFreq[r][randomData[r]] = 1;
 181                                         }
 182
 183                                         //add randoms score to validscores
 184                                         validScores[randomData[r]] = randomData[r];
 185                                 }
 186
 187                                 //update progress bar
 188                                 reading->update(j);
 189
 190                                 delete randT;
 191                         }
 192
 193                 }else {
 194                         //get pscores for random trees
 195                         for (int j = 0; j < iters; j++) {
 196                                 //create new tree with same num nodes and leaves as users
 197                                 randT = new Tree();
 198                                 //create random relationships between nodes
 199
 200                                 randT->assembleRandomTree();
 201
 202                                 //get pscore of random tree
 203                                 randomData = pars->getValues(randT);
 204
 205                                 for(int r = 0; r < numComp; r++) {
 206                                         //add trees pscore to map of scores
 207                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 208                                         if (it != rscoreFreq[r].end()) {//already have that score
 209                                                 rscoreFreq[r][randomData[r]]++;
 210                                         }else{//first time we have seen this score
 211                                                 rscoreFreq[r][randomData[r]] = 1;
 212                                         }
 213
 214                                         //add randoms score to validscores
 215                                         validScores[randomData[r]] = randomData[r];
 216                                 }
 217
 218                                 //update progress bar
 219                                 reading->update(j);
 220
 221                                 delete randT;
 222                         }
 223                 }
 224
 225                 for(int a = 0; a < numComp; a++) {
 226                         float rcumul = 0.0000;
 227                         float ucumul = 0.0000;
 228                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 229                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 230                                 if (randomtree == "") {
 231                                         map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
 232                                         //user data has that score
 233                                         if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
 234                                         else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
 235                                         //make uCumul map
 236                                         uCumul[a][it->first] = ucumul;
 237                                 }
 238
 239                                 //make rscoreFreq map and rCumul
 240                                 map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
 241                                 //get percentage of random trees with that info
 242                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
 243                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 244                                 rCumul[a][it->first] = rcumul;
 245                         }
 246
 247                         //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 248                         for (int h = 0; h < userTreeScores[a].size(); h++) {
 249                                 UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
 250                         }
 251                 }
 252
 253                 //finish progress bar
 254                 reading->finish();
 255                 delete reading;
 256
 257
 258                 printParsimonyFile();
 259                 if (randomtree == "") { printUSummaryFile(); }
 260
 261                 //reset globaldata's treemap if you just did random distrib
 262                 if (randomtree != "") {
 263                         //memory leak prevention
 264                         //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
 265                         globaldata->gTreemap = savetmap;
 266                 }
 267
 268                 //reset groups parameter
 269                 globaldata->Groups.clear();
 270
 271                 return 0;
 272
 273         }
 274         catch(exception& e) {
 275                 errorOut(e, "ParsimonyCommand", "execute");
 276                 exit(1);
 277         }
 278 }
 279
 280 /***********************************************************/
 281 void ParsimonyCommand::printParsimonyFile() {
 282         try {
 283                 vector<double> data;
 284                 vector<string> tags;
 285
 286                 if (randomtree == "") {
 287                         tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 288                 }else {
 289                         tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 290                 }
 291
 292                 for(int a = 0; a < numComp; a++) {
 293                         output->initFile(groupComb[a], tags);
 294                         //print each line
 295                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 296                                 if (randomtree == "") {
 297                                         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]);
 298                                 }else{
 299                                         data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 300                                 }
 301                                 output->output(data);
 302                                 data.clear();
 303                         }
 304                         output->resetFile();
 305                 }
 306         }
 307         catch(exception& e) {
 308                 errorOut(e, "ParsimonyCommand", "printParsimonyFile");
 309                 exit(1);
 310         }
 311 }
 312 /***********************************************************/
 313 void ParsimonyCommand::printUSummaryFile() {
 314         try {
 315                 //column headers
 316                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 317                 mothurOut("Tree#\tGroups\tParsScore\tParsSig"); mothurOutEndLine();
 318
 319                 //format output
 320                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 321
 322
 323                 //print each line
 324                 for (int i = 0; i< T.size(); i++) {
 325                         for(int a = 0; a < numComp; a++) {
 326                                 if (UScoreSig[a][i] > (1/(float)iters)) {
 327                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 328                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 329                                         mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); mothurOutEndLine();
 330                                 }else {
 331                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length())  << '\t' << "<" << (1/float(iters)) << endl;
 332                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
 333                                         mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); mothurOutEndLine();
 334                                 }
 335                         }
 336                 }
 337
 338                 outSum.close();
 339         }
 340         catch(exception& e) {
 341                 errorOut(e, "ParsimonyCommand", "printUSummaryFile");
 342                 exit(1);
 343         }
 344 }
 345
 346 /***********************************************************/
 347 void ParsimonyCommand::getUserInput() {
 348         try {
 349
 350                 //create treemap
 351                 tmap = new TreeMap();
 352
 353                 mothurOut("Please enter the number of groups you would like to analyze: ");
 354                 cin >> numGroups;
 355                 mothurOutJustToLog(toString(numGroups)); mothurOutEndLine();
 356
 357                 int num, count;
 358                 count = 1;
 359                 numEachGroup.resize(numGroups, 0);
 360
 361                 for (int i = 1; i <= numGroups; i++) {
 362                         mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
 363                         cin >> num;
 364                         mothurOutJustToLog(toString(num)); mothurOutEndLine();
 365
 366                         //set tmaps seqsPerGroup
 367                         tmap->seqsPerGroup[toString(i)] = num;
 368                         tmap->namesOfGroups.push_back(toString(i));
 369
 370                         //set tmaps namesOfSeqs
 371                         for (int j = 0; j < num; j++) {
 372                                 tmap->namesOfSeqs.push_back(toString(count));
 373                                 tmap->treemap[toString(count)].groupname = toString(i);
 374                                 count++;
 375                         }
 376                 }
 377
 378                 //clears buffer so next command doesn't have error
 379                 string s;
 380                 getline(cin, s);
 381
 382                 //save tmap for later
 383                 //memory leak prevention
 384                 //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
 385                 globaldata->gTreemap = tmap;
 386                 globaldata->Treenames = tmap->namesOfSeqs;
 387
 388         }
 389         catch(exception& e) {
 390                 errorOut(e, "ParsimonyCommand", "getUserInput");
 391                 exit(1);
 392         }
 393 }
 394
 395 /***********************************************************/
 396
 397