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][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...
  75
  76                 sumDelta.resize(numComp-numGroups, 0.0);
  77
  78                 matrix->setBounds();
  79
  80                 //load distances
  81                 if (form != "discrete") { matrix->getDist(dist); }
  82                 else {
  83                         float f = 0.0;
  84                         while (f <= cutOff) {
  85                                 dist.push_back(f);
  86                                 f += step;
  87                         }
  88                 }
  89
  90                 /*****************************/
  91                 //get values for users matrix
  92                 /*****************************/
  93
  94                 //clear out old Values
  95                 deltaValues.clear();
  96                 deltaValues.resize(dist.size());
  97
  98                 coverage->getValues(matrix, cValues, dist, "user");
  99
 100                 //loop through each distance and load rsumdelta
 101                 for (int p = 0; p < cValues.size(); p++) {
 102                         //find delta values
 103                         int count = 0;
 104                         for (int i = 0; i < numGroups; i++) {
 105                                 for (int j = 0; j < numGroups; j++) {
 106                                         //don't save AA to AA
 107                                         if (i != j) {
 108                                                 //(Caa - Cab)^2
 109                                                 deltaValues[p].push_back( (abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])) );
 110                                                 sumDelta[count] += deltaValues[p][count];
 111                                                 count++;
 112                                         }
 113                                 }
 114                         }
 115                 }
 116
 117                 printCoverageFile();
 118
 119                 /*******************************************************************************/
 120                 //create and score random matrixes finding the sumDelta values for summary file
 121                 /******************************************************************************/
 122
 123                 //initialize rsumDelta
 124                 rsumDelta.resize(numComp-numGroups);
 125                 for (int l = 0; l < rsumDelta.size(); l++) {
 126                         for (int w = 0; w < iters; w++) {
 127                                 rsumDelta[l].push_back(0.0);
 128                         }
 129                 }
 130
 131
 132                 for (int m = 0; m < iters; m++) {
 133                         //generate random matrix in getValues
 134                         //values for random matrix
 135
 136                         coverage->getValues(matrix, cValues, dist, "random");
 137
 138                         //loop through each distance and load rsumdelta
 139                         for (int p = 0; p < cValues.size(); p++) {
 140                                 //find delta values
 141                                 int count = 0;
 142                                 for (int i = 0; i < numGroups; i++) {
 143                                         for (int j = 0; j < numGroups; j++) {
 144                                                 //don't save AA to AA
 145                                                 if (i != j) {
 146                                                         //(Caa - Cab)^2
 147                                                         rsumDelta[count][m] += ((abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])));
 148                                                         count++;
 149                                                 }
 150                                         }
 151                                 }
 152
 153                         }
 154 //cout << "iter " << m << endl;
 155                         //clear out old Values
 156                         cValues.clear();
 157
 158 //cout << "random sum delta for iter " << m << endl;
 159 //for (int i = 0; i < rsumDelta.size(); i++) {
 160 //      cout << setprecision(6) << rsumDelta[i][m] << '\t';
 161 //}
 162 //cout << endl;
 163
 164                 }
 165
 166
 167                 /**********************************************************/
 168                 //find the signifigance of the user matrix' sumdelta values
 169                 /**********************************************************/
 170
 171                 for (int t = 0; t < rsumDelta.size(); t++) {
 172                         //sort rsumDelta t
 173                         sort(rsumDelta[t].begin(), rsumDelta[t].end());
 174
 175                         //the index of the score higher than yours is returned
 176                         //so if you have 1000 random matrices the index returned is 100
 177                         //then there are 900 matrices with a score greater then you.
 178                         //giving you a signifigance of 0.900
 179                         int index = findIndex(sumDelta[t], t);
 180
 181                         //the signifigance is the number of trees with the users score or higher
 182                         sumDeltaSig.push_back((iters-index)/(float)iters);
 183
 184                 }
 185
 186                 printSummaryFile();
 187
 188                 //clear out users groups
 189                 globaldata->Groups.clear();
 190
 191                 return 0;
 192         }
 193         catch(exception& e) {
 194                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 195                 exit(1);
 196         }
 197         catch(...) {
 198                 cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 199                 exit(1);
 200         }
 201 }
 202 //**********************************************************************************************************************
 203 void LibShuffCommand::printCoverageFile() {
 204         try {
 205                 //format output
 206                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 207
 208                 //loop through each distance
 209                 for (int p = 0; p < cValues.size(); p++) {
 210                         out << setprecision(6) << dist[p] << '\t';
 211                         //print out coverage values
 212                         for (int i = 0; i < numGroups; i++) {
 213                                 for (int j = 0; j < numGroups; j++) {
 214                                         out << cValues[p][i][j] << '\t';
 215                                 }
 216                         }
 217
 218                         for (int h = 0; h < deltaValues[p].size(); h++) {
 219                                 out << deltaValues[p][h] << '\t';
 220                         }
 221
 222                         out << endl;
 223                 }
 224
 225         }
 226         catch(exception& e) {
 227                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 228                 exit(1);
 229         }
 230         catch(...) {
 231                 cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 232                 exit(1);
 233         }
 234 }
 235 //**********************************************************************************************************************
 236 void LibShuffCommand::printSummaryFile() {
 237         try {
 238                 //format output
 239                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 240
 241                 for (int i = 0; i < numGroups; i++) {
 242                         for (int j = 0; j < numGroups; j++) {
 243                                 //don't output AA to AA
 244                                 if (i != j) {
 245                                         outSum << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 246                                         cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 247                                 }
 248                         }
 249                 }
 250                 outSum << endl;
 251                 cout << endl;
 252
 253                 //print out delta values
 254                 for (int i = 0; i < sumDelta.size(); i++) {
 255                         if (sumDeltaSig[i] > (1/(float)iters)) {
 256                                 outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 257                                 cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 258                         }else {
 259                                 outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
 260                                 cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
 261                         }
 262                 }
 263
 264                 outSum << endl;
 265                 cout << endl;
 266
 267         }
 268         catch(exception& e) {
 269                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 270                 exit(1);
 271         }
 272         catch(...) {
 273                 cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 274                 exit(1);
 275         }
 276 }
 277
 278 //**********************************************************************************************************************
 279 void LibShuffCommand::setGroups() {
 280         try {
 281                 //if the user has not entered specific groups to analyze then do them all
 282                 if (globaldata->Groups.size() == 0) {
 283                         numGroups = globaldata->gGroupmap->getNumGroups();
 284                         for (int i=0; i < numGroups; i++) {
 285                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 286                         }
 287                 }else {
 288                         if (globaldata->getGroups() != "all") {
 289                                 //check that groups are valid
 290                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 291                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 292                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 293                                                 // erase the invalid group from globaldata->Groups
 294                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 295                                         }
 296                                 }
 297
 298                                 //if the user only entered invalid groups
 299                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 300                                         numGroups = globaldata->gGroupmap->getNumGroups();
 301                                         for (int i=0; i < numGroups; i++) {
 302                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 303                                         }
 304                                         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;
 305                                 }else { numGroups = globaldata->Groups.size(); }
 306                         }else { //users wants all groups
 307                                 numGroups = globaldata->gGroupmap->getNumGroups();
 308                                 globaldata->Groups.clear();
 309                                 for (int i=0; i < numGroups; i++) {
 310                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 311                                 }
 312                         }
 313                 }
 314
 315                 //sort so labels match
 316                 sort(globaldata->Groups.begin(), globaldata->Groups.end());
 317
 318                 // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
 319                 for (int i=0; i<numGroups; i++) {
 320                         for (int l = 0; l < numGroups; l++) {
 321                                 //set group comparison labels
 322                                 groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
 323                         }
 324                 }
 325         }
 326         catch(exception& e) {
 327                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 328                 exit(1);
 329         }
 330         catch(...) {
 331                 cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 332                 exit(1);
 333         }
 334 }
 335 /***********************************************************/
 336 int LibShuffCommand::findIndex(float score, int index) {
 337         try{
 338                 for (int i = 0; i < rsumDelta[index].size(); i++) {
 339                         if (rsumDelta[index][i] >= score)       {       return i;       }
 340                 }
 341                 return rsumDelta[index].size();
 342         }
 343         catch(exception& e) {
 344                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 345                 exit(1);
 346         }
 347         catch(...) {
 348                 cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 349                 exit(1);
 350         }
 351 }
 352
 353 /***********************************************************/
 354