libshuffcommand.cpp

   1 /*
   2  *  libshuffcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "libshuffcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14
  15 LibShuffCommand::LibShuffCommand(){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 convert(globaldata->getCutOff(), cutOff);
  19                 convert(globaldata->getIters(), iters);
  20                 convert(globaldata->getStep(), step);
  21                 form = globaldata->getForm();
  22                 matrix = globaldata->gMatrix;
  23                 coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
  24                 summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
  25                 openOutputFile(coverageFile, out);
  26                 openOutputFile(summaryFile, outSum);
  27
  28                 //set the groups to be analyzed
  29                 setGroups();
  30
  31                 //file headers for coverage file
  32                 out << "D" << '\t';
  33                 for (int i = 0; i < groupComb.size(); i++) {
  34                         out << "C" + groupComb[i] << '\t';
  35                 }
  36
  37                 for (int i = 0; i < numGroups; i++) {
  38                         for (int j = 0; j < numGroups; j++) {
  39                                 //don't output AA to AA
  40                                 if (i != j) {
  41                                         out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
  42                                 }
  43                         }
  44                 }
  45                 out << endl;
  46
  47                 numComp = numGroups*numGroups;
  48
  49                 coverage = new Coverage();
  50
  51         }
  52         catch(exception& e) {
  53                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56         catch(...) {
  57                 cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60
  61 }
  62
  63 //**********************************************************************************************************************
  64
  65 LibShuffCommand::~LibShuffCommand(){
  66         delete coverage;
  67 }
  68
  69 //**********************************************************************************************************************
  70
  71 int LibShuffCommand::execute(){
  72         try {
  73                 //deltaValues[0] = scores for the difference between AA and AB.
  74                 //cValues[0][0] = AA, cValues[0][1] = AB, cValues[0][2] = AC, cValues[1][0] = BA, cValues[1][1] = BB...
  75                 vector<float> dist;
  76                 int next;
  77
  78                 sumDelta.resize(numComp-numGroups, 0.0);
  79
  80                 float D = 0.0;
  81
  82                 /*****************************/
  83                 //get values for users matrix
  84                 /*****************************/
  85                 matrix->setBounds();
  86
  87                 if (form != "discrete") { matrix->getDist(dist); next = 1; }
  88 //cout << "Distances" << endl;
  89 //for (int i = 0; i < dist.size(); i++) { cout << dist[i] << " "; }
  90 //cout << endl;
  91
  92                 //get values for users matrix
  93                 while (D <= cutOff) {
  94                         //clear out old Values
  95                         deltaValues.clear();
  96                         coverage->getValues(matrix, D, cValues);
  97
  98                         //find delta values
  99                         int count = 0;
 100                         for (int i = 0; i < numGroups; i++) {
 101                                 for (int j = 0; j < numGroups; j++) {
 102                                         //don't save AA to AA
 103                                         if (i != j) {
 104                                                 //(Caa - Cab)^2
 105                                                 deltaValues.push_back( (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j])) );
 106                                                 sumDelta[count] += deltaValues[count];
 107                                                 count++;
 108                                         }
 109                                 }
 110                         }
 111
 112                         printCoverageFile(D);
 113
 114                         //check form
 115                         if (form != "discrete") {
 116                                 if (next == dist.size()) { break; }
 117                                 else {  D = dist[next];  next++;        }
 118                         }else {  D += step;  }
 119
 120
 121                 }
 122
 123                 //output sum Deltas
 124                 for (int i = 0; i < numGroups; i++) {
 125                         for (int j = 0; j < numGroups; j++) {
 126                                 //don't output AA to AA
 127                                 if (i != j) {
 128                                         cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 129                                 }
 130                         }
 131                 }
 132                 cout << endl;
 133
 134                 for (int i = 0; i < sumDelta.size(); i++) {
 135                         cout << setprecision(6) << sumDelta[i] << '\t';
 136                 }
 137                 cout << endl;
 138
 139                 /*******************************************************************************/
 140                 //create and score random matrixes finding the sumDelta values for summary file
 141                 /******************************************************************************/
 142
 143                 //initialize rsumDelta
 144                 rsumDelta.resize(numComp-numGroups);
 145                 for (int l = 0; l < rsumDelta.size(); l++) {
 146                         for (int w = 0; w < iters; w++) {
 147                                 rsumDelta[l].push_back(0.0);
 148                         }
 149                 }
 150
 151
 152                 for (int m = 0; m < iters; m++) {
 153                         //generate random matrix in getValues
 154                         //values for random matrix
 155                         cout << "Iteration " << m+1 << endl;
 156                         D = 0.0;
 157                         next = 1;
 158
 159                         while (D <= cutOff) {
 160                                 coverage->getValues(matrix, D, cValues, "random");
 161
 162                                 //find delta values
 163                                 int count = 0;
 164                                 for (int i = 0; i < numGroups; i++) {
 165                                         for (int j = 0; j < numGroups; j++) {
 166                                                 //don't save AA to AA
 167                                                 if (i != j) {
 168                                                         //(Caa - Cab)^2
 169                                                         rsumDelta[count][m] += ((abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j])));
 170 //cout << "iter " << m << " box " << i << j << " delta = " << ((abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j]))) << endl;
 171                                                         count++;
 172                                                 }
 173                                         }
 174                                 }
 175
 176                                 //check form
 177                                 if (form != "discrete") {
 178                                         if (next == dist.size()) { break; }
 179                                         else {  D = dist[next];  next++;        }
 180                                 }else {  D += step;  }
 181
 182
 183                                 //clear out old Values
 184                                 cValues.clear();
 185                         }
 186 cout << "random sum delta for iter " << m << endl;
 187 for (int i = 0; i < rsumDelta.size(); i++) {
 188         cout << setprecision(6) << rsumDelta[i][m] << '\t';
 189 }
 190 cout << endl;
 191
 192                 }
 193
 194                 /**********************************************************/
 195                 //find the signifigance of the user matrix' sumdelta values
 196                 /**********************************************************/
 197
 198                 for (int t = 0; t < rsumDelta.size(); t++) {
 199                         //sort rsumDelta t
 200                         sort(rsumDelta[t].begin(), rsumDelta[t].end());
 201
 202                         //the index of the score higher than yours is returned
 203                         //so if you have 1000 random matrices the index returned is 100
 204                         //then there are 900 matrices with a score greater then you.
 205                         //giving you a signifigance of 0.900
 206                         int index = findIndex(sumDelta[t], t);
 207
 208                         //the signifigance is the number of trees with the users score or higher
 209                         sumDeltaSig.push_back((iters-index)/(float)iters);
 210
 211                 }
 212
 213                 printSummaryFile();
 214
 215                 //clear out users groups
 216                 globaldata->Groups.clear();
 217
 218                 return 0;
 219         }
 220         catch(exception& e) {
 221                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 222                 exit(1);
 223         }
 224         catch(...) {
 225                 cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 226                 exit(1);
 227         }
 228 }
 229 //**********************************************************************************************************************
 230 void LibShuffCommand::printCoverageFile(float d) {
 231         try {
 232                 //format output
 233                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 234
 235                 out << setprecision(6) << d << '\t';
 236
 237                 //print out coverage values
 238                 for (int i = 0; i < numGroups; i++) {
 239                         for (int j = 0; j < numGroups; j++) {
 240                                 out << cValues[i][j] << '\t';
 241                         }
 242                 }
 243
 244                 //print out delta values
 245                 for (int i = 0; i < deltaValues.size(); i++) {
 246                         out << deltaValues[i] << '\t';
 247                 }
 248
 249                 out << endl;
 250
 251         }
 252         catch(exception& e) {
 253                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 254                 exit(1);
 255         }
 256         catch(...) {
 257                 cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 258                 exit(1);
 259         }
 260 }
 261 //**********************************************************************************************************************
 262 void LibShuffCommand::printSummaryFile() {
 263         try {
 264                 //format output
 265                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 266
 267                 for (int i = 0; i < numGroups; i++) {
 268                         for (int j = 0; j < numGroups; j++) {
 269                                 //don't output AA to AA
 270                                 if (i != j) {
 271                                         outSum << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 272                                         cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 273                                 }
 274                         }
 275                 }
 276                 outSum << endl;
 277                 cout << endl;
 278
 279                 //print out delta values
 280                 for (int i = 0; i < sumDelta.size(); i++) {
 281                         outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 282                         cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 283                 }
 284
 285                 outSum << endl;
 286                 cout << endl;
 287
 288         }
 289         catch(exception& e) {
 290                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 291                 exit(1);
 292         }
 293         catch(...) {
 294                 cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 295                 exit(1);
 296         }
 297 }
 298
 299 //**********************************************************************************************************************
 300 void LibShuffCommand::setGroups() {
 301         try {
 302                 //if the user has not entered specific groups to analyze then do them all
 303                 if (globaldata->Groups.size() == 0) {
 304                         numGroups = globaldata->gGroupmap->getNumGroups();
 305                         for (int i=0; i < numGroups; i++) {
 306                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 307                         }
 308                 }else {
 309                         if (globaldata->getGroups() != "all") {
 310                                 //check that groups are valid
 311                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 312                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 313                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 314                                                 // erase the invalid group from globaldata->Groups
 315                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 316                                         }
 317                                 }
 318
 319                                 //if the user only entered invalid groups
 320                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 321                                         numGroups = globaldata->gGroupmap->getNumGroups();
 322                                         for (int i=0; i < numGroups; i++) {
 323                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 324                                         }
 325                                         cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 326                                 }else { numGroups = globaldata->Groups.size(); }
 327                         }else { //users wants all groups
 328                                 numGroups = globaldata->gGroupmap->getNumGroups();
 329                                 globaldata->Groups.clear();
 330                                 for (int i=0; i < numGroups; i++) {
 331                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 332                                 }
 333                         }
 334                 }
 335
 336                 //sort so labels match
 337                 sort(globaldata->Groups.begin(), globaldata->Groups.end());
 338
 339                 // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
 340                 for (int i=0; i<numGroups; i++) {
 341                         for (int l = 0; l < numGroups; l++) {
 342                                 //set group comparison labels
 343                                 groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
 344                         }
 345                 }
 346         }
 347         catch(exception& e) {
 348                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 349                 exit(1);
 350         }
 351         catch(...) {
 352                 cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 353                 exit(1);
 354         }
 355 }
 356 /***********************************************************/
 357 int LibShuffCommand::findIndex(float score, int index) {
 358         try{
 359                 for (int i = 0; i < rsumDelta[index].size(); i++) {
 360                         if (rsumDelta[index][i] >= score)       {       return i;       }
 361                 }
 362                 return rsumDelta[index].size();
 363         }
 364         catch(exception& e) {
 365                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 366                 exit(1);
 367         }
 368         catch(...) {
 369                 cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 370                 exit(1);
 371         }
 372 }
 373
 374 /***********************************************************/
 375