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() {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16
  17                 //randomtree will tell us if user had their own treefile or if they just want the random distribution
  18                 randomtree = globaldata->getRandomTree();
  19
  20                 //user has entered their own tree
  21                 if (randomtree == "") {
  22                         T = globaldata->gTree;
  23                         tmap = globaldata->gTreemap;
  24                         parsFile = globaldata->getTreeFile() + ".parsimony";
  25                         openOutputFile(parsFile, out);
  26                         sumFile = globaldata->getTreeFile() + ".psummary";
  27                         openOutputFile(sumFile, outSum);
  28                         distFile = globaldata->getTreeFile() + ".pdistrib";
  29                         openOutputFile(distFile, outDist);
  30                         //set users groups to analyze
  31                         setGroups();
  32                 }else { //user wants random distribution
  33                         savetmap = globaldata->gTreemap;
  34                         getUserInput();
  35                         parsFile = randomtree + ".rd_parsimony";
  36                         openOutputFile(parsFile, out);
  37                 }
  38
  39                 convert(globaldata->getIters(), iters);  //how many random trees to generate
  40                 pars = new Parsimony(tmap);
  41
  42         }
  43         catch(exception& e) {
  44                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  45                 exit(1);
  46         }
  47         catch(...) {
  48                 cout << "An unknown error has occurred in the ParsimonyCommand class function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  49                 exit(1);
  50         }
  51 }
  52 /***********************************************************/
  53 int ParsimonyCommand::execute() {
  54         try {
  55
  56                 //get pscore for users tree
  57                 userData.resize(1,0);  //data[0] = pscore.
  58                 randomData.resize(1,0);  //data[0] = pscore.
  59
  60                 //format output
  61                 outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
  62                 outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
  63
  64                 if (randomtree == "") {
  65                         //get pscores for users trees
  66                         for (int i = 0; i < T.size(); i++) {
  67                                 cout << "Processing tree " << i+1 << endl;
  68                                 userData = pars->getValues(T[i]);  //userData[0] = pscore
  69                                 cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
  70                                 //update uscoreFreq
  71                                 it = uscoreFreq.find(userData[0]);
  72                                 if (it == uscoreFreq.end()) {//new score
  73                                         uscoreFreq[userData[0]] = 1;
  74                                 }else{ uscoreFreq[userData[0]]++; }
  75
  76                                 //add users score to valid scores
  77                                 validScores[userData[0]] = userData[0];
  78
  79                                 //save score for summary file
  80                                 userTreeScores.push_back(userData[0]);
  81
  82                         }
  83
  84                         //get pscores for random trees
  85                         for (int j = 0; j < iters; j++) {
  86                                 //create new tree with same num nodes and leaves as users
  87                                 randT = new Tree();
  88                                 //create random relationships between nodes
  89                                 randT->assembleRandomTree();
  90                                 //get pscore of random tree
  91                                 randomData = pars->getValues(randT);
  92
  93                                 //add trees pscore to map of scores
  94                                 it2 = rscoreFreq.find(randomData[0]);
  95                                 if (it2 != rscoreFreq.end()) {//already have that score
  96                                         rscoreFreq[randomData[0]]++;
  97                                 }else{//first time we have seen this score
  98                                         rscoreFreq[randomData[0]] = 1;
  99                                 }
 100
 101                                 //add randoms score to validscores
 102                                 validScores[randomData[0]] = randomData[0];
 103
 104                                 //output info to pdistrib file
 105                                 outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
 106
 107                                 delete randT;
 108                         }
 109                 }else {
 110                         //get pscores for random trees
 111                         for (int j = 0; j < iters; j++) {
 112                                 //create new tree with same num nodes and leaves as users
 113                                 randT = new Tree();
 114                                 //create random relationships between nodes
 115                                 randT->assembleRandomTree();
 116                                 //get pscore of random tree
 117                                 randomData = pars->getValues(randT);
 118
 119                                 //add trees pscore to map of scores
 120                                 it2 = rscoreFreq.find(randomData[0]);
 121                                 if (it2 != rscoreFreq.end()) {//already have that score
 122                                         rscoreFreq[randomData[0]]++;
 123                                 }else{//first time we have seen this score
 124                                         rscoreFreq[randomData[0]] = 1;
 125                                 }
 126
 127                                 //add randoms score to validscores
 128                                 validScores[randomData[0]] = randomData[0];
 129
 130                                 delete randT;
 131                         }
 132                 }
 133
 134                 float rcumul = 0.0000;
 135                 float ucumul = 0.0000;
 136
 137                 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 138                 for (it = validScores.begin(); it != validScores.end(); it++) {
 139                         if (randomtree == "") {
 140                                 it2 = uscoreFreq.find(it->first);
 141                                 //user data has that score
 142                                 if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second;  }
 143                                 else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
 144                                 //make uCumul map
 145                                 uCumul[it->first] = ucumul;
 146                         }
 147
 148                         //make rscoreFreq map and rCumul
 149                         it2 = rscoreFreq.find(it->first);
 150                         //get percentage of random trees with that info
 151                         if (it2 != rscoreFreq.end()) {  rscoreFreq[it->first] /= iters; rcumul+= it2->second;  }
 152                         else { rscoreFreq[it->first] = 0.0000; } //no random trees with that score
 153                         rCumul[it->first] = rcumul;
 154                 }
 155
 156                 //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 157                 for (int h = 0; h < userTreeScores.size(); h++) {
 158                         UScoreSig.push_back(rCumul[userTreeScores[h]]);
 159                 }
 160
 161                 printParsimonyFile();
 162                 printUSummaryFile();
 163
 164                 //reset globaldata's treemap if you just did random distrib
 165                 if (randomtree != "") { globaldata->gTreemap = savetmap; }
 166
 167                 //reset randomTree parameter to ""
 168                 globaldata->setRandomTree("");
 169                 //reset groups parameter
 170                 globaldata->Groups.clear();
 171
 172                 return 0;
 173
 174         }
 175         catch(exception& e) {
 176                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179         catch(...) {
 180                 cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 181                 exit(1);
 182         }
 183 }
 184
 185 /***********************************************************/
 186 void ParsimonyCommand::printParsimonyFile() {
 187         try {
 188                 //column headers
 189                 if (randomtree == "") {
 190                         out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 191                 }else {
 192                         out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 193                 }
 194
 195                 //format output
 196                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 197
 198                 //print each line
 199                 for (it = validScores.begin(); it != validScores.end(); it++) {
 200                         if (randomtree == "") {
 201                                 out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
 202                         }else{
 203                                 out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
 204                         }
 205                 }
 206
 207                 out.close();
 208
 209         }
 210         catch(exception& e) {
 211                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214         catch(...) {
 215                 cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 216                 exit(1);
 217         }
 218 }
 219 /***********************************************************/
 220 void ParsimonyCommand::printUSummaryFile() {
 221         try {
 222                 //column headers
 223                 outSum << "Tree#" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
 224
 225                 //format output
 226                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 227
 228                 //print each line
 229                 for (int i = 0; i< T.size(); i++) {
 230                         outSum << setprecision(6) << i+1 << '\t' << '\t' << userTreeScores[i] << '\t' << UScoreSig[i] << endl;
 231                 }
 232
 233                 outSum.close();
 234         }
 235         catch(exception& e) {
 236                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 237                 exit(1);
 238         }
 239         catch(...) {
 240                 cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243 }
 244
 245 /***********************************************************/
 246 void ParsimonyCommand::getUserInput() {
 247         try {
 248
 249                 //create treemap
 250                 tmap = new TreeMap();
 251
 252                 cout << "Please enter the number of groups you would like to analyze: ";
 253                 cin >> numGroups;
 254
 255                 int num, count;
 256                 count = 1;
 257                 numEachGroup.resize(numGroups, 0);
 258
 259                 for (int i = 1; i <= numGroups; i++) {
 260                         cout << "Please enter the number of sequences in group " << i <<  ": ";
 261                         cin >> num;
 262
 263                         //set tmaps seqsPerGroup
 264                         tmap->seqsPerGroup[toString(i)] = num;
 265
 266                         //set tmaps namesOfSeqs
 267                         for (int j = 0; j < num; j++) {
 268                                 tmap->namesOfSeqs.push_back(toString(count));
 269                                 tmap->treemap[toString(count)].groupname = toString(i);
 270                                 count++;
 271                         }
 272                 }
 273
 274                 //clears buffer so next command doesn't have error
 275                 string s;
 276                 getline(cin, s);
 277
 278                 //save tmap for later
 279                 globaldata->gTreemap = tmap;
 280
 281         }
 282         catch(exception& e) {
 283                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 284                 exit(1);
 285         }
 286         catch(...) {
 287                 cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 288                 exit(1);
 289         }
 290 }
 291 /***********************************************************/
 292
 293 void ParsimonyCommand::setGroups() {
 294         try {
 295                 //if the user has not entered specific groups to analyze then do them all
 296                 if (globaldata->Groups.size() != 0) {
 297                         //check that groups are valid
 298                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 299                                 if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 300                                         cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 301                                         // erase the invalid group from globaldata->Groups
 302                                         globaldata->Groups.erase (globaldata->Groups.begin()+i);
 303                                 }
 304                         }
 305
 306                         //if the user only entered invalid groups
 307                         if (globaldata->Groups.size() == 0) {
 308                                 cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
 309                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 310                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 311                                 }
 312                         }
 313
 314                 }else {
 315                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 316                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 317                         }
 318                 }
 319         }
 320         catch(exception& e) {
 321                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 322                 exit(1);
 323         }
 324         catch(...) {
 325                 cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 326                 exit(1);
 327         }
 328
 329 }
 330 /*****************************************************************/
 331
 332