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