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                         copyUserTree = new Tree();
  66                         //get pscores for users trees
  67                         for (int i = 0; i < T.size(); i++) {
  68                                 //copy users tree so that you can redo pgroups
  69                                 copyUserTree->getCopy(T[i]);
  70                                 cout << "Processing tree " << i+1 << endl;
  71                                 userData = pars->getValues(copyUserTree);  //userData[0] = pscore
  72                                 cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
  73                                 //update uscoreFreq
  74                                 it = uscoreFreq.find(userData[0]);
  75                                 if (it == uscoreFreq.end()) {//new score
  76                                         uscoreFreq[userData[0]] = 1;
  77                                 }else{ uscoreFreq[userData[0]]++; }
  78
  79                                 //add users score to valid scores
  80                                 validScores[userData[0]] = userData[0];
  81
  82                                 //save score for summary file
  83                                 userTreeScores.push_back(userData[0]);
  84
  85                         }
  86
  87                         //get pscores for random trees
  88                         for (int j = 0; j < iters; j++) {
  89                                 //create new tree with same num nodes and leaves as users
  90                                 randT = new Tree();
  91                                 //create random relationships between nodes
  92                                 randT->assembleRandomTree();
  93                                 //get pscore of random tree
  94                                 randomData = pars->getValues(randT);
  95
  96                                 //add trees pscore to map of scores
  97                                 it2 = rscoreFreq.find(randomData[0]);
  98                                 if (it2 != rscoreFreq.end()) {//already have that score
  99                                         rscoreFreq[randomData[0]]++;
 100                                 }else{//first time we have seen this score
 101                                         rscoreFreq[randomData[0]] = 1;
 102                                 }
 103
 104                                 //add randoms score to validscores
 105                                 validScores[randomData[0]] = randomData[0];
 106
 107                                 //output info to pdistrib file
 108                                 outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
 109
 110                                 delete randT;
 111                         }
 112                 }else {
 113                         //get pscores for random trees
 114                         for (int j = 0; j < iters; j++) {
 115                                 //create new tree with same num nodes and leaves as users
 116                                 randT = new Tree();
 117                                 //create random relationships between nodes
 118                                 randT->assembleRandomTree();
 119                                 //get pscore of random tree
 120                                 randomData = pars->getValues(randT);
 121
 122                                 //add trees pscore to map of scores
 123                                 it2 = rscoreFreq.find(randomData[0]);
 124                                 if (it2 != rscoreFreq.end()) {//already have that score
 125                                         rscoreFreq[randomData[0]]++;
 126                                 }else{//first time we have seen this score
 127                                         rscoreFreq[randomData[0]] = 1;
 128                                 }
 129
 130                                 //add randoms score to validscores
 131                                 validScores[randomData[0]] = randomData[0];
 132
 133                                 delete randT;
 134                         }
 135                 }
 136
 137                 float rcumul = 0.0000;
 138                 float ucumul = 0.0000;
 139
 140                 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 141                 for (it = validScores.begin(); it != validScores.end(); it++) {
 142                         if (randomtree == "") {
 143                                 it2 = uscoreFreq.find(it->first);
 144                                 //user data has that score
 145                                 if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second;  }
 146                                 else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
 147                                 //make uCumul map
 148                                 uCumul[it->first] = ucumul;
 149                         }
 150
 151                         //make rscoreFreq map and rCumul
 152                         it2 = rscoreFreq.find(it->first);
 153                         //get percentage of random trees with that info
 154                         if (it2 != rscoreFreq.end()) {  rscoreFreq[it->first] /= iters; rcumul+= it2->second;  }
 155                         else { rscoreFreq[it->first] = 0.0000; } //no random trees with that score
 156                         rCumul[it->first] = rcumul;
 157                 }
 158
 159                 //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 160                 for (int h = 0; h < userTreeScores.size(); h++) {
 161                         UScoreSig.push_back(rCumul[userTreeScores[h]]);
 162                 }
 163
 164                 printParsimonyFile();
 165                 printUSummaryFile();
 166
 167                 //reset globaldata's treemap if you just did random distrib
 168                 if (randomtree != "") { globaldata->gTreemap = savetmap; }
 169
 170                 //reset randomTree parameter to ""
 171                 globaldata->setRandomTree("");
 172                 //reset groups parameter
 173                 globaldata->Groups.clear();
 174
 175                 return 0;
 176
 177         }
 178         catch(exception& e) {
 179                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 180                 exit(1);
 181         }
 182         catch(...) {
 183                 cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 184                 exit(1);
 185         }
 186 }
 187
 188 /***********************************************************/
 189 void ParsimonyCommand::printParsimonyFile() {
 190         try {
 191                 //column headers
 192                 if (randomtree == "") {
 193                         out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 194                 }else {
 195                         out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 196                 }
 197
 198                 //format output
 199                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 200
 201                 //print each line
 202                 for (it = validScores.begin(); it != validScores.end(); it++) {
 203                         if (randomtree == "") {
 204                                 out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
 205                         }else{
 206                                 out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
 207                         }
 208                 }
 209
 210                 out.close();
 211
 212         }
 213         catch(exception& e) {
 214                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 215                 exit(1);
 216         }
 217         catch(...) {
 218                 cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 219                 exit(1);
 220         }
 221 }
 222 /***********************************************************/
 223 void ParsimonyCommand::printUSummaryFile() {
 224         try {
 225                 //column headers
 226                 outSum << "Tree#" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
 227
 228                 //format output
 229                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 230
 231                 //print each line
 232                 for (int i = 0; i< T.size(); i++) {
 233                         outSum << setprecision(6) << i+1 << '\t' << '\t' << userTreeScores[i] << '\t' << UScoreSig[i] << endl;
 234                 }
 235
 236                 outSum.close();
 237         }
 238         catch(exception& e) {
 239                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 240                 exit(1);
 241         }
 242         catch(...) {
 243                 cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 244                 exit(1);
 245         }
 246 }
 247
 248 /***********************************************************/
 249 void ParsimonyCommand::getUserInput() {
 250         try {
 251
 252                 //create treemap
 253                 tmap = new TreeMap();
 254
 255                 cout << "Please enter the number of groups you would like to analyze: ";
 256                 cin >> numGroups;
 257
 258                 int num, count;
 259                 count = 1;
 260                 numEachGroup.resize(numGroups, 0);
 261
 262                 for (int i = 1; i <= numGroups; i++) {
 263                         cout << "Please enter the number of sequences in group " << i <<  ": ";
 264                         cin >> num;
 265
 266                         //set tmaps seqsPerGroup
 267                         tmap->seqsPerGroup[toString(i)] = num;
 268
 269                         //set tmaps namesOfSeqs
 270                         for (int j = 0; j < num; j++) {
 271                                 tmap->namesOfSeqs.push_back(toString(count));
 272                                 tmap->treemap[toString(count)].groupname = toString(i);
 273                                 count++;
 274                         }
 275                 }
 276
 277                 //clears buffer so next command doesn't have error
 278                 string s;
 279                 getline(cin, s);
 280
 281                 //save tmap for later
 282                 globaldata->gTreemap = tmap;
 283
 284         }
 285         catch(exception& e) {
 286                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 287                 exit(1);
 288         }
 289         catch(...) {
 290                 cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 291                 exit(1);
 292         }
 293 }
 294 /***********************************************************/
 295
 296 void ParsimonyCommand::setGroups() {
 297         try {
 298                 //if the user has not entered specific groups to analyze then do them all
 299                 if (globaldata->Groups.size() != 0) {
 300                         //check that groups are valid
 301                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 302                                 if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
 303                                         cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 304                                         // erase the invalid group from globaldata->Groups
 305                                         globaldata->Groups.erase (globaldata->Groups.begin()+i);
 306                                 }
 307                         }
 308
 309                         //if the user only entered invalid groups
 310                         if (globaldata->Groups.size() == 0) {
 311                                 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;
 312                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 313                                         globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 314                                 }
 315                         }
 316
 317                 }else {
 318                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 319                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 320                         }
 321                 }
 322         }
 323         catch(exception& e) {
 324                 cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 325                 exit(1);
 326         }
 327         catch(...) {
 328                 cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 329                 exit(1);
 330         }
 331
 332 }
 333 /*****************************************************************/
 334
 335