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 /* This class is designed to implement an integral form of the Cramer-von Mises statistic.
  11         you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
  12         paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
  13         DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
  14
  15
  16 #include "libshuffcommand.h"
  17
  18 //**********************************************************************************************************************
  19
  20
  21 LibShuffCommand::LibShuffCommand(){
  22         try {
  23                 globaldata = GlobalData::getInstance();
  24                 convert(globaldata->getCutOff(), cutOff);
  25                 convert(globaldata->getIters(), iters);
  26                 convert(globaldata->getStep(), step);
  27                 form = globaldata->getForm();
  28                 matrix = globaldata->gMatrix;
  29                 coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
  30                 summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
  31                 openOutputFile(coverageFile, out);
  32                 openOutputFile(summaryFile, outSum);
  33
  34                 //set the groups to be analyzed
  35                 setGroups();
  36
  37                 //file headers for coverage file
  38                 out << "D" << '\t';
  39                 for (int i = 0; i < groupComb.size(); i++) {
  40                         out << "C" + groupComb[i] << '\t';
  41                 }
  42
  43                 for (int i = 0; i < numGroups; i++) {
  44                         for (int j = 0; j < numGroups; j++) {
  45                                 //don't output AA to AA
  46                                 if (i != j) {
  47                                         out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
  48                                 }
  49                         }
  50                 }
  51                 out << endl;
  52
  53                 numComp = numGroups*numGroups;
  54
  55                 coverage = new Coverage();
  56
  57         }
  58         catch(exception& e) {
  59                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  60                 exit(1);
  61         }
  62         catch(...) {
  63                 cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  64                 exit(1);
  65         }
  66
  67 }
  68
  69 //**********************************************************************************************************************
  70
  71 LibShuffCommand::~LibShuffCommand(){
  72         delete coverage;
  73 }
  74
  75 //**********************************************************************************************************************
  76
  77 int LibShuffCommand::execute(){
  78         try {
  79                 //deltaValues[0] = scores for the difference between AA and AB.
  80                 //cValues[0][0][0] = AA at distance 0.0, cValues[0][0][1] = AB at distance 0.0, cValues[0][0][2] = AC at distance 0.0, cValues[0][1][0] = BA at distance 0.0, cValues[0][1][1] = BB...
  81                 Progress* reading;
  82                 reading = new Progress("Comparing to random:", iters);
  83
  84                 sumDelta.resize(numComp-numGroups, 0.0);
  85
  86                 matrix->setBounds();
  87
  88                 //load distances
  89                 if (form != "discrete") { matrix->getDist(dist); }
  90                 else {
  91                         float f = 0.0;
  92                         while (f <= cutOff) {
  93                                 dist.push_back(f);
  94                                 f += step;
  95                         }
  96                 }
  97
  98                 /*****************************/
  99                 //get values for users matrix
 100                 /*****************************/
 101
 102                 //clear out old Values
 103                 deltaValues.clear();
 104                 deltaValues.resize(dist.size());
 105
 106                 coverage->getValues(matrix, cValues, dist, "user");
 107
 108                 //loop through each distance and load rsumdelta
 109                 for (int p = 0; p < cValues.size(); p++) {
 110                         //find delta values
 111                         int count = 0;
 112                         for (int i = 0; i < numGroups; i++) {
 113                                 for (int j = 0; j < numGroups; j++) {
 114                                         //don't save AA to AA
 115                                         if (i != j) {
 116                                                 //(Caa - Cab)^2
 117                                                 deltaValues[p].push_back((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j]));
 118                                                 sumDelta[count] += deltaValues[p][count];
 119                                                 count++;
 120                                         }
 121                                 }
 122                         }
 123                 }
 124
 125                 printCoverageFile();
 126
 127                 /*******************************************************************************/
 128                 //create and score random matrixes finding the sumDelta values for summary file
 129                 /******************************************************************************/
 130
 131                 //initialize rsumDelta
 132                 rsumDelta.resize(numComp-numGroups);
 133                 for (int l = 0; l < rsumDelta.size(); l++) {
 134                         for (int w = 0; w < iters; w++) {
 135                                 rsumDelta[l].push_back(0.0);
 136                         }
 137                 }
 138
 139
 140                 for (int m = 0; m < iters; m++) {
 141                         //generate random matrix in getValues
 142                         //values for random matrix
 143
 144                         coverage->getValues(matrix, cValues, dist, "random");
 145
 146                         //loop through each distance and load rsumdelta
 147                         for (int p = 0; p < cValues.size(); p++) {
 148                                 //find delta values
 149                                 int count = 0;
 150                                 for (int i = 0; i < numGroups; i++) {
 151                                         for (int j = 0; j < numGroups; j++) {
 152                                                 //don't save AA to AA
 153                                                 if (i != j) {
 154                                                         //(Caa - Cab)^2
 155                                                         rsumDelta[count][m] += ((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j]));
 156                                                         count++;
 157                                                 }
 158                                         }
 159                                 }
 160
 161                         }
 162
 163                         //clear out old Values
 164                         reading->update(m);
 165                         cValues.clear();
 166
 167                 }
 168
 169                 reading->finish();
 170                 delete reading;
 171
 172                 /**********************************************************/
 173                 //find the signifigance of the user matrix' sumdelta values
 174                 /**********************************************************/
 175
 176                 for (int t = 0; t < rsumDelta.size(); t++) {
 177                         //sort rsumDelta t
 178                         sort(rsumDelta[t].begin(), rsumDelta[t].end());
 179
 180                         //the index of the score higher than yours is returned
 181                         //so if you have 1000 random matrices the index returned is 100
 182                         //then there are 900 matrices with a score greater then you.
 183                         //giving you a signifigance of 0.900
 184                         int index = findIndex(sumDelta[t], t);
 185
 186                         //the signifigance is the number of trees with the users score or higher
 187                         sumDeltaSig.push_back((iters-index)/(float)iters);
 188
 189                 }
 190
 191                 printSummaryFile();
 192
 193                 //clear out users groups
 194                 globaldata->Groups.clear();
 195
 196                 return 0;
 197         }
 198         catch(exception& e) {
 199                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202         catch(...) {
 203                 cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 204                 exit(1);
 205         }
 206 }
 207 //**********************************************************************************************************************
 208 void LibShuffCommand::printCoverageFile() {
 209         try {
 210                 //format output
 211                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 212
 213                 //loop through each distance
 214                 for (int p = 0; p < cValues.size(); p++) {
 215                         out << setprecision(6) << dist[p] << '\t';
 216                         //print out coverage values
 217                         for (int i = 0; i < numGroups; i++) {
 218                                 for (int j = 0; j < numGroups; j++) {
 219                                         out << cValues[p][i][j] << '\t';
 220                                 }
 221                         }
 222
 223                         for (int h = 0; h < deltaValues[p].size(); h++) {
 224                                 out << deltaValues[p][h] << '\t';
 225                         }
 226
 227                         out << endl;
 228                 }
 229
 230         }
 231         catch(exception& e) {
 232                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 233                 exit(1);
 234         }
 235         catch(...) {
 236                 cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 237                 exit(1);
 238         }
 239 }
 240 //**********************************************************************************************************************
 241 void LibShuffCommand::printSummaryFile() {
 242         try {
 243                 //format output
 244                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 245
 246                 for (int i = 0; i < numGroups; i++) {
 247                         for (int j = 0; j < numGroups; j++) {
 248                                 //don't output AA to AA
 249                                 if (i != j) {
 250                                         outSum << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 251                                         cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 252                                 }
 253                         }
 254                 }
 255                 outSum << endl;
 256                 cout << endl;
 257
 258                 //print out delta values
 259                 for (int i = 0; i < sumDelta.size(); i++) {
 260                         if (sumDeltaSig[i] > (1/(float)iters)) {
 261                                 outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 262                                 cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 263                         }else {
 264                                 outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
 265                                 cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
 266                         }
 267                 }
 268
 269                 outSum << endl;
 270                 cout << endl;
 271
 272         }
 273         catch(exception& e) {
 274                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 275                 exit(1);
 276         }
 277         catch(...) {
 278                 cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 279                 exit(1);
 280         }
 281 }
 282
 283 //**********************************************************************************************************************
 284 void LibShuffCommand::setGroups() {
 285         try {
 286                 //if the user has not entered specific groups to analyze then do them all
 287                 if (globaldata->Groups.size() == 0) {
 288                         numGroups = globaldata->gGroupmap->getNumGroups();
 289                         for (int i=0; i < numGroups; i++) {
 290                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 291                         }
 292                 }else {
 293                         if (globaldata->getGroups() != "all") {
 294                                 //check that groups are valid
 295                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 296                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 297                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 298                                                 // erase the invalid group from globaldata->Groups
 299                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 300                                         }
 301                                 }
 302
 303                                 //if the user only entered invalid groups
 304                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 305                                         numGroups = globaldata->gGroupmap->getNumGroups();
 306                                         for (int i=0; i < numGroups; i++) {
 307                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 308                                         }
 309                                         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;
 310                                 }else { numGroups = globaldata->Groups.size(); }
 311                         }else { //users wants all groups
 312                                 numGroups = globaldata->gGroupmap->getNumGroups();
 313                                 globaldata->Groups.clear();
 314                                 for (int i=0; i < numGroups; i++) {
 315                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 316                                 }
 317                         }
 318                 }
 319
 320                 //sort so labels match
 321                 sort(globaldata->Groups.begin(), globaldata->Groups.end());
 322
 323                 // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
 324                 for (int i=0; i<numGroups; i++) {
 325                         for (int l = 0; l < numGroups; l++) {
 326                                 //set group comparison labels
 327                                 groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
 328                         }
 329                 }
 330         }
 331         catch(exception& e) {
 332                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 333                 exit(1);
 334         }
 335         catch(...) {
 336                 cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 337                 exit(1);
 338         }
 339 }
 340 /***********************************************************/
 341 int LibShuffCommand::findIndex(float score, int index) {
 342         try{
 343                 for (int i = 0; i < rsumDelta[index].size(); i++) {
 344                         if (rsumDelta[index][i] >= score)       {       return i;       }
 345                 }
 346                 return rsumDelta[index].size();
 347         }
 348         catch(exception& e) {
 349                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. 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 LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 354                 exit(1);
 355         }
 356 }
 357
 358 /***********************************************************/
 359