weighted.cpp

   1 /*
   2  *  weighted.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "weighted.h"
  11
  12 /**************************************************************************************************/
  13
  14 EstOutput Weighted::getValues(Tree* t, int p, string o) {
  15     try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 data.clear(); //clear out old values
  19                 int numGroups;
  20                 vector<double> D;
  21                 processors = p;
  22                 outputDir = o;
  23
  24                 numGroups = globaldata->Groups.size();
  25
  26                 vector<double> sums = getBranchLengthSums(t);
  27
  28                 if (m->control_pressed) { return data; }
  29
  30                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
  31                 vector< vector<string> > namesOfGroupCombos;
  32                 for (int i=0; i<numGroups; i++) {
  33                         for (int l = i+1; l < numGroups; l++) {
  34                                 //initialize weighted scores
  35                                 //WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
  36                                 vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
  37                                 namesOfGroupCombos.push_back(groups);
  38                         }
  39                 }
  40
  41                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  42                         if(processors == 1){
  43                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums);
  44                         }else{
  45                                 int numPairs = namesOfGroupCombos.size();
  46
  47                                 int numPairsPerProcessor = numPairs / processors;
  48
  49                                 for (int i = 0; i < processors; i++) {
  50                                         int startPos = i * numPairsPerProcessor;
  51                                         if(i == processors - 1){
  52                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
  53                                         }
  54                                         lines.push_back(new linePair(startPos, numPairsPerProcessor));
  55                                 }
  56
  57                                 data = createProcesses(t, namesOfGroupCombos, sums);
  58
  59                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
  60                         }
  61                 #else
  62                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums);
  63                 #endif
  64
  65                 return data;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "Weighted", "getValues");
  69                 exit(1);
  70         }
  71 }
  72 /**************************************************************************************************/
  73
  74 EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums) {
  75         try {
  76 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  77                 int process = 1;
  78                 int num = 0;
  79                 vector<int> processIDS;
  80
  81                 EstOutput results;
  82
  83                 //loop through and create all the processes you want
  84                 while (process != processors) {
  85                         int pid = fork();
  86
  87                         if (pid > 0) {
  88                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
  89                                 process++;
  90                         }else if (pid == 0){
  91
  92                                 EstOutput Myresults;
  93                                 Myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
  94
  95                                 m->mothurOut("Merging results."); m->mothurOutEndLine();
  96
  97                                 //pass numSeqs to parent
  98                                 ofstream out;
  99
 100                                 string tempFile = outputDir + toString(getpid()) + ".weighted.results.temp";
 101
 102                                 m->openOutputFile(tempFile, out);
 103
 104                                 out << Myresults.size() << endl;
 105                                 for (int i = 0; i < Myresults.size(); i++) {  out << Myresults[i] << '\t';  } out << endl;
 106                                 out.close();
 107
 108                                 exit(0);
 109                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 110                 }
 111
 112                 results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums);
 113
 114                 //force parent to wait until all the processes are done
 115                 for (int i=0;i<(processors-1);i++) {
 116                         int temp = processIDS[i];
 117                         wait(&temp);
 118                 }
 119
 120                 if (m->control_pressed) { return results; }
 121
 122                 //get data created by processes
 123                 for (int i=0;i<(processors-1);i++) {
 124                         ifstream in;
 125                         string s = outputDir + toString(processIDS[i]) + ".weighted.results.temp";
 126                         m->openInputFile(s, in);
 127
 128                         //get quantiles
 129                         while (!in.eof()) {
 130                                 int num;
 131                                 in >> num; m->gobble(in);
 132
 133                                 if (m->control_pressed) { break; }
 134
 135                                 double w;
 136                                 for (int j = 0; j < num; j++) {
 137                                         in >> w;
 138                                         results.push_back(w);
 139                                 }
 140                                 m->gobble(in);
 141                         }
 142                         in.close();
 143                         remove(s.c_str());
 144                 }
 145
 146                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 147
 148                 return results;
 149 #endif
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "Weighted", "createProcesses");
 153                 exit(1);
 154         }
 155 }
 156 /**************************************************************************************************/
 157 EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums) {
 158  try {
 159                 EstOutput results;
 160                 vector<double> D;
 161
 162                 int count = 0;
 163                 for (int h = start; h < (start+num); h++) {
 164
 165                         if (m->control_pressed) { return results; }
 166
 167                         //initialize weighted score
 168                         string groupA = namesOfGroupCombos[h][0];
 169                         string groupB = namesOfGroupCombos[h][1];
 170
 171                         WScore[groupA+groupB] = 0.0;
 172                         D.push_back(0.0000); //initialize a spot in D for each combination
 173
 174                         //adding the wieghted sums from group i
 175                         for (int j = 0; j < t->groupNodeInfo[groupA].size(); j++) { //the leaf nodes that have seqs from group i
 176                                 map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupA][j]].pcount.find(groupA);
 177                                 int numSeqsInGroupI = it->second;
 178
 179                                 double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groupA][j]]) / (double)tmap->seqsPerGroup[groupA]);
 180
 181                                 D[count] += weightedSum;
 182                         }
 183
 184                         //adding the wieghted sums from group l
 185                         for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l
 186                                 map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
 187                                 int numSeqsInGroupL = it->second;
 188
 189                                 double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groupB][j]]) / (double)tmap->seqsPerGroup[groupB]);
 190
 191                                 D[count] += weightedSum;
 192                         }
 193                         count++;
 194                 }
 195
 196                 //calculate u for the group comb
 197                 int total = t->getNumNodes();
 198                 int twentyPercent = (total * 0.20);
 199                 for(int i=0;i<t->getNumNodes();i++){
 200                         for (int h = start; h < (start+num); h++) {
 201
 202                                 string groupA = namesOfGroupCombos[h][0];
 203                                 string groupB = namesOfGroupCombos[h][1];
 204
 205                                 if (m->control_pressed) { return results; }
 206
 207                                 double u;
 208                                 //does this node have descendants from groupA
 209                                 it = t->tree[i].pcount.find(groupA);
 210                                 //if it does u = # of its descendants with a certain group / total number in tree with a certain group
 211                                 if (it != t->tree[i].pcount.end()) {
 212                                         u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
 213                                 }else { u = 0.00; }
 214
 215
 216                                 //does this node have descendants from group l
 217                                 it = t->tree[i].pcount.find(groupB);
 218                                 //if it does subtract their percentage from u
 219                                 if (it != t->tree[i].pcount.end()) {
 220                                         u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
 221                                 }
 222
 223                                 u = abs(u * t->tree[i].getBranchLength());
 224
 225                                 //save groupcombs u value
 226                                 WScore[(groupA+groupB)] += u;
 227                         }
 228                         //report progress
 229                         if((i) % twentyPercent == 0){   m->mothurOut("Percentage complete: " + toString(int((i / (float)total) * 100.0))); m->mothurOutEndLine();               }
 230                 }
 231
 232                 m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
 233
 234                 /********************************************************/
 235                 //calculate weighted score for the group combination
 236                 double UN;
 237                 count = 0;
 238                 for (int h = start; h < (start+num); h++) {
 239                         UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
 240
 241                         if (isnan(UN) || isinf(UN)) { UN = 0; }
 242                         results.push_back(UN);
 243                         count++;
 244                 }
 245
 246                 return results;
 247         }
 248         catch(exception& e) {
 249                 m->errorOut(e, "Weighted", "driver");
 250                 exit(1);
 251         }
 252 }
 253 /**************************************************************************************************/
 254 EstOutput Weighted::getValues(Tree* t, string groupA, string groupB, vector<double>& sums) {
 255  try {
 256                 globaldata = GlobalData::getInstance();
 257
 258                 data.clear(); //clear out old values
 259
 260                 if (m->control_pressed) { return data; }
 261
 262                 //initialize weighted score
 263                 WScore[(groupA+groupB)] = 0.0;
 264                 double D = 0.0;
 265
 266                 vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
 267
 268                 //adding the wieghted sums from group i
 269                 for (int j = 0; j < t->groupNodeInfo[groups[0]].size(); j++) { //the leaf nodes that have seqs from group i
 270                         map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[0]][j]].pcount.find(groups[0]);
 271                         int numSeqsInGroupI = it->second;
 272
 273                         double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groups[0]][j]]) / (double)tmap->seqsPerGroup[groups[0]]);
 274
 275                         D += weightedSum;
 276                 }
 277
 278                 //adding the wieghted sums from group l
 279                 for (int j = 0; j < t->groupNodeInfo[groups[1]].size(); j++) { //the leaf nodes that have seqs from group l
 280                         map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[1]][j]].pcount.find(groups[1]);
 281                         int numSeqsInGroupL = it->second;
 282
 283                         double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groups[1]][j]]) / (double)tmap->seqsPerGroup[groups[1]]);
 284
 285                         D += weightedSum;
 286                 }
 287
 288                 //calculate u for the group comb
 289                 for(int i=0;i<t->getNumNodes();i++){
 290
 291                         if (m->control_pressed) { return data; }
 292
 293                         double u;
 294                         //does this node have descendants from groupA
 295                         it = t->tree[i].pcount.find(groupA);
 296                         //if it does u = # of its descendants with a certain group / total number in tree with a certain group
 297                         if (it != t->tree[i].pcount.end()) {
 298                                 u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
 299                         }else { u = 0.00; }
 300
 301
 302                         //does this node have descendants from group l
 303                         it = t->tree[i].pcount.find(groupB);
 304                         //if it does subtract their percentage from u
 305                         if (it != t->tree[i].pcount.end()) {
 306                                 u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
 307                         }
 308
 309                         u = abs(u * t->tree[i].getBranchLength());
 310
 311                         //save groupcombs u value
 312                         WScore[(groupA+groupB)] += u;
 313                 }
 314
 315                 /********************************************************/
 316
 317                 //calculate weighted score for the group combination
 318                 double UN;
 319                 UN = (WScore[(groupA+groupB)] / D);
 320
 321                 if (isnan(UN) || isinf(UN)) { UN = 0; }
 322                 data.push_back(UN);
 323
 324                 return data;
 325         }
 326         catch(exception& e) {
 327                 m->errorOut(e, "Weighted", "getValues");
 328                 exit(1);
 329         }
 330 }
 331 /**************************************************************************************************/
 332 vector<double> Weighted::getBranchLengthSums(Tree* t) {
 333         try {
 334
 335                 vector<double> sums;
 336
 337                 for(int v=0;v<t->getNumLeaves();v++){
 338
 339                         if (m->control_pressed) { return sums; }
 340
 341                         int index = v;
 342                         double sum = 0.0000;
 343
 344                         //while you aren't at root
 345                         while(t->tree[index].getParent() != -1){
 346
 347                                 //if you have a BL
 348                                 if(t->tree[index].getBranchLength() != -1){
 349                                         sum += abs(t->tree[index].getBranchLength());
 350                                 }
 351                                 index = t->tree[index].getParent();
 352                         }
 353
 354                         //get last breanch length added
 355                         if(t->tree[index].getBranchLength() != -1){
 356                                 sum += abs(t->tree[index].getBranchLength());
 357                         }
 358
 359                         sums.push_back(sum);
 360                 }
 361
 362                 return sums;
 363         }
 364         catch(exception& e) {
 365                 m->errorOut(e, "Weighted", "getBranchLengthSums");
 366                 exit(1);
 367         }
 368 }
 369 /**************************************************************************************************/
 370
 371
 372