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                                 EstOutput Myresults;
  92                                 Myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
  93
  94                                 if (m->control_pressed) { exit(0); }
  95
  96                                 m->mothurOut("Merging results."); m->mothurOutEndLine();
  97
  98                                 //pass numSeqs to parent
  99                                 ofstream out;
 100                                 string tempFile = outputDir + toString(getpid()) + ".weighted.results.temp";
 101                                 m->openOutputFile(tempFile, out);
 102                                 out << Myresults.size() << endl;
 103                                 for (int i = 0; i < Myresults.size(); i++) {  out << Myresults[i] << '\t';  } out << endl;
 104                                 out.close();
 105
 106                                 exit(0);
 107                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 108                 }
 109
 110                 results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums);
 111
 112                 //force parent to wait until all the processes are done
 113                 for (int i=0;i<(processors-1);i++) {
 114                         int temp = processIDS[i];
 115                         wait(&temp);
 116                 }
 117
 118                 if (m->control_pressed) { return results; }
 119
 120                 //get data created by processes
 121                 for (int i=0;i<(processors-1);i++) {
 122                         ifstream in;
 123                         string s = outputDir + toString(processIDS[i]) + ".weighted.results.temp";
 124                         m->openInputFile(s, in);
 125
 126                         //get quantiles
 127                         while (!in.eof()) {
 128                                 int num;
 129                                 in >> num; m->gobble(in);
 130
 131                                 if (m->control_pressed) { break; }
 132
 133                                 double w;
 134                                 for (int j = 0; j < num; j++) {
 135                                         in >> w;
 136                                         results.push_back(w);
 137                                 }
 138                                 m->gobble(in);
 139                         }
 140                         in.close();
 141                         remove(s.c_str());
 142                 }
 143
 144                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 145
 146                 return results;
 147 #endif
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "Weighted", "createProcesses");
 151                 exit(1);
 152         }
 153 }
 154 /**************************************************************************************************/
 155 EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums) {
 156  try {
 157                 globaldata = GlobalData::getInstance();
 158
 159                 EstOutput results;
 160                 vector<double> D;
 161
 162                 int count = 0;
 163                 int total = num;
 164                 int twentyPercent = (total * 0.20);
 165
 166                 for (int h = start; h < (start+num); h++) {
 167
 168                         if (m->control_pressed) { return results; }
 169
 170                         //initialize weighted score
 171                         string groupA = namesOfGroupCombos[h][0];
 172                         string groupB = namesOfGroupCombos[h][1];
 173
 174                         WScore[groupA+groupB] = 0.0;
 175                         D.push_back(0.0000); //initialize a spot in D for each combination
 176
 177                         //adding the wieghted sums from group i
 178                         for (int j = 0; j < t->groupNodeInfo[groupA].size(); j++) { //the leaf nodes that have seqs from group i
 179                                 map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupA][j]].pcount.find(groupA);
 180                                 int numSeqsInGroupI = it->second;
 181
 182                                 double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groupA][j]]) / (double)tmap->seqsPerGroup[groupA]);
 183
 184                                 D[count] += weightedSum;
 185                         }
 186
 187                         //adding the wieghted sums from group l
 188                         for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l
 189                                 map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
 190                                 int numSeqsInGroupL = it->second;
 191
 192                                 double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groupB][j]]) / (double)tmap->seqsPerGroup[groupB]);
 193
 194                                 D[count] += weightedSum;
 195                         }
 196                         count++;
 197
 198                         //report progress
 199                         if((count) % twentyPercent == 0){       m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine();           }
 200                 }
 201
 202                 m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
 203
 204                 //calculate u for the group comb
 205                 for(int i=0;i<t->getNumNodes();i++){
 206                         for (int h = start; h < (start+num); h++) {
 207
 208                                 string groupA = namesOfGroupCombos[h][0];
 209                                 string groupB = namesOfGroupCombos[h][1];
 210
 211                                 if (m->control_pressed) { return results; }
 212
 213                                 double u;
 214                                 //does this node have descendants from groupA
 215                                 it = t->tree[i].pcount.find(groupA);
 216                                 //if it does u = # of its descendants with a certain group / total number in tree with a certain group
 217                                 if (it != t->tree[i].pcount.end()) {
 218                                         u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
 219                                 }else { u = 0.00; }
 220
 221
 222                                 //does this node have descendants from group l
 223                                 it = t->tree[i].pcount.find(groupB);
 224                                 //if it does subtract their percentage from u
 225                                 if (it != t->tree[i].pcount.end()) {
 226                                         u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
 227                                 }
 228
 229                                 u = abs(u * t->tree[i].getBranchLength());
 230
 231                                 //save groupcombs u value
 232                                 WScore[(groupA+groupB)] += u;
 233                         }
 234                 }
 235
 236                 /********************************************************/
 237
 238                 //calculate weighted score for the group combination
 239                 double UN;
 240                 count = 0;
 241                 for (int h = start; h < (start+num); h++) {
 242                         UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
 243
 244                         if (isnan(UN) || isinf(UN)) { UN = 0; }
 245                         results.push_back(UN);
 246                         count++;
 247                 }
 248
 249                 return results;
 250         }
 251         catch(exception& e) {
 252                 m->errorOut(e, "Weighted", "driver");
 253                 exit(1);
 254         }
 255 }
 256 /**************************************************************************************************/
 257 EstOutput Weighted::getValues(Tree* t, string groupA, string groupB, vector<double>& sums) {
 258  try {
 259                 globaldata = GlobalData::getInstance();
 260
 261                 data.clear(); //clear out old values
 262
 263                 if (m->control_pressed) { return data; }
 264
 265                 //initialize weighted score
 266                 WScore[(groupA+groupB)] = 0.0;
 267                 double D = 0.0;
 268
 269                 vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
 270
 271                 //adding the wieghted sums from group i
 272                 for (int j = 0; j < t->groupNodeInfo[groups[0]].size(); j++) { //the leaf nodes that have seqs from group i
 273                         map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[0]][j]].pcount.find(groups[0]);
 274                         int numSeqsInGroupI = it->second;
 275
 276                         double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groups[0]][j]]) / (double)tmap->seqsPerGroup[groups[0]]);
 277
 278                         D += weightedSum;
 279                 }
 280
 281                 //adding the wieghted sums from group l
 282                 for (int j = 0; j < t->groupNodeInfo[groups[1]].size(); j++) { //the leaf nodes that have seqs from group l
 283                         map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[1]][j]].pcount.find(groups[1]);
 284                         int numSeqsInGroupL = it->second;
 285
 286                         double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groups[1]][j]]) / (double)tmap->seqsPerGroup[groups[1]]);
 287
 288                         D += weightedSum;
 289                 }
 290
 291                 //calculate u for the group comb
 292                 for(int i=0;i<t->getNumNodes();i++){
 293
 294                         if (m->control_pressed) { return data; }
 295
 296                         double u;
 297                         //does this node have descendants from groupA
 298                         it = t->tree[i].pcount.find(groupA);
 299                         //if it does u = # of its descendants with a certain group / total number in tree with a certain group
 300                         if (it != t->tree[i].pcount.end()) {
 301                                 u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
 302                         }else { u = 0.00; }
 303
 304
 305                         //does this node have descendants from group l
 306                         it = t->tree[i].pcount.find(groupB);
 307                         //if it does subtract their percentage from u
 308                         if (it != t->tree[i].pcount.end()) {
 309                                 u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
 310                         }
 311
 312                         u = abs(u * t->tree[i].getBranchLength());
 313
 314                         //save groupcombs u value
 315                         WScore[(groupA+groupB)] += u;
 316                 }
 317
 318                 /********************************************************/
 319
 320                 //calculate weighted score for the group combination
 321                 double UN;
 322                 UN = (WScore[(groupA+groupB)] / D);
 323
 324                 if (isnan(UN) || isinf(UN)) { UN = 0; }
 325                 data.push_back(UN);
 326
 327                 return data;
 328         }
 329         catch(exception& e) {
 330                 m->errorOut(e, "Weighted", "getValues");
 331                 exit(1);
 332         }
 333 }
 334 /**************************************************************************************************/
 335 vector<double> Weighted::getBranchLengthSums(Tree* t) {
 336         try {
 337
 338                 vector<double> sums;
 339
 340                 for(int v=0;v<t->getNumLeaves();v++){
 341
 342                         if (m->control_pressed) { return sums; }
 343
 344                         int index = v;
 345                         double sum = 0.0000;
 346
 347                         //while you aren't at root
 348                         while(t->tree[index].getParent() != -1){
 349
 350                                 //if you have a BL
 351                                 if(t->tree[index].getBranchLength() != -1){
 352                                         sum += abs(t->tree[index].getBranchLength());
 353                                 }
 354                                 index = t->tree[index].getParent();
 355                         }
 356
 357                         //get last breanch length added
 358                         if(t->tree[index].getBranchLength() != -1){
 359                                 sum += abs(t->tree[index].getBranchLength());
 360                         }
 361
 362                         sums.push_back(sum);
 363                 }
 364
 365                 return sums;
 366         }
 367         catch(exception& e) {
 368                 m->errorOut(e, "Weighted", "getBranchLengthSums");
 369                 exit(1);
 370         }
 371 }
 372 /**************************************************************************************************/
 373
 374
 375