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                 matrix = globaldata->gMatrix;
  21                 coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
  22                 summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
  23                 openOutputFile(coverageFile, out);
  24                 openOutputFile(summaryFile, outSum);
  25
  26                 //set the groups to be analyzed
  27                 setGroups();
  28
  29                 //file headers for coverage file
  30                 out << "D" << '\t';
  31                 for (int i = 0; i < groupComb.size(); i++) {
  32                         out << "C" + groupComb[i] << '\t';
  33                 }
  34
  35                 for (int i = 0; i < numGroups; i++) {
  36                         for (int j = 0; j < numGroups; j++) {
  37                                 //don't output AA to AA
  38                                 if (i != j) {
  39                                         out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
  40                                 }
  41                         }
  42                 }
  43                 out << endl;
  44
  45                 numComp = numGroups*numGroups;
  46
  47                 coverage = new Coverage();
  48
  49         }
  50         catch(exception& e) {
  51                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  52                 exit(1);
  53         }
  54         catch(...) {
  55                 cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58
  59 }
  60
  61 //**********************************************************************************************************************
  62
  63 LibShuffCommand::~LibShuffCommand(){
  64         delete coverage;
  65 }
  66
  67 //**********************************************************************************************************************
  68
  69 int LibShuffCommand::execute(){
  70         try {
  71                 //deltaValues[0] = scores for the difference between AA and AB.
  72                 //cValues[0][0] = AA, cValues[0][1] = AB, cValues[0][2] = AC, cValues[1][0] = BA, cValues[1][1] = BB...
  73
  74                 sumDelta.resize(numComp-numGroups, 0.0);
  75
  76                 float D = 0.0;
  77
  78                 /*****************************/
  79                 //get values for users matrix
  80                 /*****************************/
  81                 matrix->getMinsForRowsVectors();
  82
  83                 //get values for users matrix
  84                 while (D <= cutOff) {
  85                         cValues = coverage->getValues(matrix, D);
  86
  87                         //find delta values
  88                         int count = 0;
  89                         for (int i = 0; i < numGroups; i++) {
  90                                 for (int j = 0; j < numGroups; j++) {
  91                                         //don't save AA to AA
  92                                         if (i != j) {
  93                                                 //(Caa - Cab)^2
  94                                                 deltaValues.push_back( (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j])) );
  95                                                 sumDelta[count] += deltaValues[count];
  96                                                 count++;
  97                                         }
  98                                 }
  99                         }
 100
 101                         D += 0.01;
 102
 103                         printCoverageFile(D);
 104
 105                         //clear out old Values
 106                         cValues.clear();
 107                         deltaValues.clear();
 108                 }
 109
 110                 /*******************************************************************************/
 111                 //create and score random matrixes finding the sumDelta values for summary file
 112                 /******************************************************************************/
 113
 114                 //initialize rsumDelta
 115                 rsumDelta.resize(numComp-numGroups);
 116                 for (int l = 0; l < rsumDelta.size(); l++) {
 117                         for (int w = 0; w < iters; w++) {
 118                                 rsumDelta[l].push_back(0.0);
 119                         }
 120                 }
 121
 122                 for (int m = 0; m < iters; m++) {
 123                         //generate random matrix in getValues
 124                         //values for random matrix
 125                         while (D <= cutOff) {
 126                                 cValues = coverage->getValues(matrix, D);
 127
 128                                 //find delta values
 129                                 int count = 0;
 130                                 for (int i = 0; i < numGroups; i++) {
 131                                         for (int j = 0; j < numGroups; j++) {
 132                                                 //don't save AA to AA
 133                                                 if (i != j) {
 134                                                         //(Caa - Cab)^2
 135                                                         rsumDelta[count][m] += (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j]));
 136                                                         count++;
 137                                                 }
 138                                         }
 139                                 }
 140
 141                                 D += 0.01;
 142
 143                                 //clear out old Values
 144                                 cValues.clear();
 145                         }
 146                 }
 147
 148                 /**********************************************************/
 149                 //find the signifigance of the user matrix' sumdelta values
 150                 /**********************************************************/
 151
 152                 for (int t = 0; t < rsumDelta.size(); t++) {
 153                         //sort rsumDelta t
 154                         sort(rsumDelta[t].begin(), rsumDelta[t].end());
 155
 156                         //the index of the score higher than yours is returned
 157                         //so if you have 1000 random matrices the index returned is 100
 158                         //then there are 900 matrices with a score greater then you.
 159                         //giving you a signifigance of 0.900
 160                         int index = findIndex(sumDelta[t], t);
 161
 162                         //the signifigance is the number of trees with the users score or higher
 163                         sumDeltaSig.push_back((iters-index)/(float)iters);
 164
 165                 }
 166
 167                 printSummaryFile();
 168
 169                 //clear out users groups
 170                 globaldata->Groups.clear();
 171
 172                 return 0;
 173         }
 174         catch(exception& e) {
 175                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 176                 exit(1);
 177         }
 178         catch(...) {
 179                 cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 180                 exit(1);
 181         }
 182 }
 183 //**********************************************************************************************************************
 184 void LibShuffCommand::printCoverageFile(float d) {
 185         try {
 186                 //format output
 187                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 188
 189                 out << setprecision(globaldata->getIters().length()) << d << '\t';
 190
 191                 //print out coverage values
 192                 for (int i = 0; i < numGroups; i++) {
 193                         for (int j = 0; j < numGroups; j++) {
 194                                 out << cValues[i][j] << '\t';
 195                         }
 196                 }
 197
 198                 //print out delta values
 199                 for (int i = 0; i < deltaValues.size(); i++) {
 200                         out << deltaValues[i] << '\t';
 201                 }
 202
 203                 out << endl;
 204
 205         }
 206         catch(exception& e) {
 207                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210         catch(...) {
 211                 cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214 }
 215 //**********************************************************************************************************************
 216 void LibShuffCommand::printSummaryFile() {
 217         try {
 218                 //format output
 219                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 220
 221                 for (int i = 0; i < numGroups; i++) {
 222                         for (int j = 0; j < numGroups; j++) {
 223                                 //don't output AA to AA
 224                                 if (i != j) {
 225                                         outSum << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
 226                                 }
 227                         }
 228                 }
 229                 outSum << endl;
 230
 231                 //print out delta values
 232                 for (int i = 0; i < sumDelta.size(); i++) {
 233                         outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
 234                 }
 235
 236                 outSum << endl;
 237
 238         }
 239         catch(exception& e) {
 240                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243         catch(...) {
 244                 cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247 }
 248
 249 //**********************************************************************************************************************
 250 void LibShuffCommand::setGroups() {
 251         try {
 252                 //if the user has not entered specific groups to analyze then do them all
 253                 if (globaldata->Groups.size() == 0) {
 254                         numGroups = globaldata->gGroupmap->getNumGroups();
 255                         for (int i=0; i < numGroups; i++) {
 256                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 257                         }
 258                 }else {
 259                         if (globaldata->getGroups() != "all") {
 260                                 //check that groups are valid
 261                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 262                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 263                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 264                                                 // erase the invalid group from globaldata->Groups
 265                                                 globaldata->Groups.erase (globaldata->Groups.begin()+i);
 266                                         }
 267                                 }
 268
 269                                 //if the user only entered invalid groups
 270                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 271                                         numGroups = globaldata->gGroupmap->getNumGroups();
 272                                         for (int i=0; i < numGroups; i++) {
 273                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 274                                         }
 275                                         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;
 276                                 }else { numGroups = globaldata->Groups.size(); }
 277                         }else { //users wants all groups
 278                                 numGroups = globaldata->gGroupmap->getNumGroups();
 279                                 globaldata->Groups.clear();
 280                                 for (int i=0; i < numGroups; i++) {
 281                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 282                                 }
 283                         }
 284                 }
 285
 286                 // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
 287                 for (int i=0; i<numGroups; i++) {
 288                         for (int l = 0; l < numGroups; l++) {
 289                                 //set group comparison labels
 290                                 groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
 291                         }
 292                 }
 293         }
 294         catch(exception& e) {
 295                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 296                 exit(1);
 297         }
 298         catch(...) {
 299                 cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 300                 exit(1);
 301         }
 302 }
 303 /***********************************************************/
 304 int LibShuffCommand::findIndex(float score, int index) {
 305         try{
 306                 for (int i = 0; i < rsumDelta[index].size(); i++) {
 307                         if (rsumDelta[index][i] >= score)       {       return i;       }
 308                 }
 309                 return rsumDelta[index].size();
 310         }
 311         catch(exception& e) {
 312                 cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 313                 exit(1);
 314         }
 315         catch(...) {
 316                 cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 317                 exit(1);
 318         }
 319 }
 320
 321 /***********************************************************/
 322