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                         parser = new OptionParser();
  28                         parser->parse(option, parameters);  delete parser;
  29
  30                         ValidParameters* validParameter = new ValidParameters();
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (it4 = parameters.begin(); it4 != parameters.end(); it4++) {
  34                                 if (validParameter->isValidParameter(it4->first, myArray, it4->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                                         cout << "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." << endl; 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 = ""; }
  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                         delete validParameter;
  58
  59                         if (abort == false) {
  60                                 //randomtree will tell us if user had their own treefile or if they just want the random distribution
  61                                 //user has entered their own tree
  62                                 if (randomtree == "") {
  63                                         T = globaldata->gTree;
  64                                         tmap = globaldata->gTreemap;
  65                                         output = new ColumnFile(globaldata->getTreeFile()  +  ".parsimony", itersString);
  66                                         sumFile = globaldata->getTreeFile() + ".psummary";
  67                                         openOutputFile(sumFile, outSum);
  68                                 }else { //user wants random distribution
  69                                         savetmap = globaldata->gTreemap;
  70                                         getUserInput();
  71                                         output = new ColumnFile(randomtree, itersString);
  72                                 }
  73
  74                                 //set users groups to analyze
  75                                 util = new SharedUtil();
  76                                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");   //sets the groups the user wants to analyze
  77                                 util->getCombos(groupComb, globaldata->Groups, numComp);
  78
  79                                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
  80
  81                                 pars = new Parsimony(tmap);
  82                                 counter = 0;
  83
  84                         }
  85
  86                 }
  87
  88         }
  89         catch(exception& e) {
  90                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  91                 exit(1);
  92         }
  93         catch(...) {
  94                 cout << "An unknown error has occurred in the ParsimonyCommand class function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  95                 exit(1);
  96         }
  97 }
  98
  99 //**********************************************************************************************************************
 100
 101 void ParsimonyCommand::help(){
 102         try {
 103                 cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
 104                 cout << "The parsimony command parameters are random, groups and iters.  No parameters are required." << "\n";
 105                 cout << "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";
 106                 cout << "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";
 107                 cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
 108                 cout << "Example parsimony(random=out, iters=500)." << "\n";
 109                 cout << "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";
 110                 cout << "and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual." << "\n";
 111                 cout << "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename)." << "\n" << "\n";
 112         }
 113         catch(exception& e) {
 114                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 115                 exit(1);
 116         }
 117         catch(...) {
 118                 cout << "An unknown error has occurred in the ParsimonyCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121 }
 122
 123
 124 /***********************************************************/
 125 int ParsimonyCommand::execute() {
 126         try {
 127
 128                 if (abort == true) { return 0; }
 129
 130                 Progress* reading;
 131                 reading = new Progress("Comparing to random:", iters);
 132
 133                 //get pscore for users tree
 134                 userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 135                 randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 136                 rscoreFreq.resize(numComp);
 137                 uscoreFreq.resize(numComp);
 138                 rCumul.resize(numComp);
 139                 uCumul.resize(numComp);
 140                 userTreeScores.resize(numComp);
 141                 UScoreSig.resize(numComp);
 142
 143                 if (randomtree == "") {
 144                         //get pscores for users trees
 145                         for (int i = 0; i < T.size(); i++) {
 146                                 userData = pars->getValues(T[i]);  //data = AB, AC, BC, ABC.
 147
 148                                 //output scores for each combination
 149                                 for(int k = 0; k < numComp; k++) {
 150
 151                                         //update uscoreFreq
 152                                         it = uscoreFreq[k].find(userData[k]);
 153                                         if (it == uscoreFreq[k].end()) {//new score
 154                                                 uscoreFreq[k][userData[k]] = 1;
 155                                         }else{ uscoreFreq[k][userData[k]]++; }
 156
 157                                         //add users score to valid scores
 158                                         validScores[userData[k]] = userData[k];
 159
 160                                         //save score for summary file
 161                                         userTreeScores[k].push_back(userData[k]);
 162                                 }
 163                         }
 164
 165                         //get pscores for random trees
 166                         for (int j = 0; j < iters; j++) {
 167                                 //create new tree with same num nodes and leaves as users
 168                                 randT = new Tree();
 169
 170                                 //create random relationships between nodes
 171                                 randT->assembleRandomTree();
 172
 173                                 //get pscore of random tree
 174                                 randomData = pars->getValues(randT);
 175
 176                                 for(int r = 0; r < numComp; r++) {
 177                                         //add trees pscore to map of scores
 178                                         it2 = rscoreFreq[r].find(randomData[r]);
 179                                         if (it2 != rscoreFreq[r].end()) {//already have that score
 180                                                 rscoreFreq[r][randomData[r]]++;
 181                                         }else{//first time we have seen this score
 182                                                 rscoreFreq[r][randomData[r]] = 1;
 183                                         }
 184
 185                                         //add randoms score to validscores
 186                                         validScores[randomData[r]] = randomData[r];
 187                                 }
 188
 189                                 //update progress bar
 190                                 reading->update(j);
 191
 192                                 delete randT;
 193                         }
 194
 195                 }else {
 196                         //get pscores for random trees
 197                         for (int j = 0; j < iters; j++) {
 198                                 //create new tree with same num nodes and leaves as users
 199                                 randT = new Tree();
 200                                 //create random relationships between nodes
 201
 202                                 randT->assembleRandomTree();
 203
 204                                 //get pscore of random tree
 205                                 randomData = pars->getValues(randT);
 206
 207                                 for(int r = 0; r < numComp; r++) {
 208                                         //add trees pscore to map of scores
 209                                         it2 = rscoreFreq[r].find(randomData[r]);
 210                                         if (it2 != rscoreFreq[r].end()) {//already have that score
 211                                                 rscoreFreq[r][randomData[r]]++;
 212                                         }else{//first time we have seen this score
 213                                                 rscoreFreq[r][randomData[r]] = 1;
 214                                         }
 215
 216                                         //add randoms score to validscores
 217                                         validScores[randomData[r]] = randomData[r];
 218                                 }
 219
 220                                 //update progress bar
 221                                 reading->update(j);
 222
 223                                 delete randT;
 224                         }
 225                 }
 226
 227                 for(int a = 0; a < numComp; a++) {
 228                         float rcumul = 0.0000;
 229                         float ucumul = 0.0000;
 230                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 231                         for (it = validScores.begin(); it != validScores.end(); it++) {
 232                                 if (randomtree == "") {
 233                                         it2 = uscoreFreq[a].find(it->first);
 234                                         //user data has that score
 235                                         if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
 236                                         else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
 237                                         //make uCumul map
 238                                         uCumul[a][it->first] = ucumul;
 239                                 }
 240
 241                                 //make rscoreFreq map and rCumul
 242                                 it2 = rscoreFreq[a].find(it->first);
 243                                 //get percentage of random trees with that info
 244                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
 245                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 246                                 rCumul[a][it->first] = rcumul;
 247                         }
 248
 249                         //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 250                         for (int h = 0; h < userTreeScores[a].size(); h++) {
 251                                 UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
 252                         }
 253                 }
 254
 255                 //finish progress bar
 256                 reading->finish();
 257                 delete reading;
 258
 259
 260                 printParsimonyFile();
 261                 if (randomtree == "") { printUSummaryFile(); }
 262
 263                 //reset globaldata's treemap if you just did random distrib
 264                 if (randomtree != "") {
 265                         //memory leak prevention
 266                         //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
 267                         globaldata->gTreemap = savetmap;
 268                 }
 269
 270                 //reset groups parameter
 271                 globaldata->Groups.clear();
 272
 273                 return 0;
 274
 275         }
 276         catch(exception& e) {
 277                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 278                 exit(1);
 279         }
 280         catch(...) {
 281                 cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 282                 exit(1);
 283         }
 284 }
 285
 286 /***********************************************************/
 287 void ParsimonyCommand::printParsimonyFile() {
 288         try {
 289                 vector<double> data;
 290                 vector<string> tags;
 291
 292                 if (randomtree == "") {
 293                         tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 294                 }else {
 295                         tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 296                 }
 297
 298                 for(int a = 0; a < numComp; a++) {
 299                         output->initFile(groupComb[a], tags);
 300                         //print each line
 301                         for (it = validScores.begin(); it != validScores.end(); it++) {
 302                                 if (randomtree == "") {
 303                                         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]);
 304                                 }else{
 305                                         data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 306                                 }
 307                                 output->output(data);
 308                                 data.clear();
 309                         }
 310                         output->resetFile();
 311                 }
 312         }
 313         catch(exception& e) {
 314                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 315                 exit(1);
 316         }
 317         catch(...) {
 318                 cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 319                 exit(1);
 320         }
 321 }
 322 /***********************************************************/
 323 void ParsimonyCommand::printUSummaryFile() {
 324         try {
 325                 //column headers
 326                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 327                 cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 328
 329                 //format output
 330                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 331
 332
 333                 //print each line
 334                 for (int i = 0; i< T.size(); i++) {
 335                         for(int a = 0; a < numComp; a++) {
 336                                 if (UScoreSig[a][i] > (1/(float)iters)) {
 337                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 338                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 339                                 }else {
 340                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length())  << '\t' << "<" << (1/float(iters)) << endl;
 341                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
 342                                 }
 343                         }
 344                 }
 345
 346                 outSum.close();
 347         }
 348         catch(exception& e) {
 349                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 350                 exit(1);
 351         }
 352         catch(...) {
 353                 cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 354                 exit(1);
 355         }
 356 }
 357
 358 /***********************************************************/
 359 void ParsimonyCommand::getUserInput() {
 360         try {
 361
 362                 //create treemap
 363                 tmap = new TreeMap();
 364
 365                 cout << "Please enter the number of groups you would like to analyze: ";
 366                 cin >> numGroups;
 367
 368                 int num, count;
 369                 count = 1;
 370                 numEachGroup.resize(numGroups, 0);
 371
 372                 for (int i = 1; i <= numGroups; i++) {
 373                         cout << "Please enter the number of sequences in group " << i <<  ": ";
 374                         cin >> num;
 375
 376                         //set tmaps seqsPerGroup
 377                         tmap->seqsPerGroup[toString(i)] = num;
 378                         tmap->namesOfGroups.push_back(toString(i));
 379
 380                         //set tmaps namesOfSeqs
 381                         for (int j = 0; j < num; j++) {
 382                                 tmap->namesOfSeqs.push_back(toString(count));
 383                                 tmap->treemap[toString(count)].groupname = toString(i);
 384                                 count++;
 385                         }
 386                 }
 387
 388                 //clears buffer so next command doesn't have error
 389                 string s;
 390                 getline(cin, s);
 391
 392                 //save tmap for later
 393                 //memory leak prevention
 394                 //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
 395                 globaldata->gTreemap = tmap;
 396                 globaldata->Treenames = tmap->namesOfSeqs;
 397
 398         }
 399         catch(exception& e) {
 400                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 401                 exit(1);
 402         }
 403         catch(...) {
 404                 cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 405                 exit(1);
 406         }
 407 }
 408
 409 /***********************************************************/
 410
 411