unweighted.cpp

   1 /*
   2  *  unweighted.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 "unweighted.h"
  11
  12 /**************************************************************************************************/
  13
  14 EstOutput Unweighted::getValues(Tree* t, int p, string o) {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 processors = p;
  18                 outputDir = o;
  19
  20                 //if the users enters no groups then give them the score of all groups
  21                 int numGroups = globaldata->Groups.size();
  22
  23                 //calculate number of comparsions
  24                 int numComp = 0;
  25                 vector< vector<string> > namesOfGroupCombos;
  26                 for (int r=0; r<numGroups; r++) {
  27                         for (int l = 0; l < r; l++) {
  28                                 numComp++;
  29                                 vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
  30                                 namesOfGroupCombos.push_back(groups);
  31                         }
  32                 }
  33
  34                 if (numComp != 1) {
  35                         vector<string> groups;
  36                         if (numGroups == 0) {
  37                                 //get score for all users groups
  38                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
  39                                         if (tmap->namesOfGroups[i] != "xxx") {
  40                                                 groups.push_back(tmap->namesOfGroups[i]);
  41                                         }
  42                                 }
  43                                 namesOfGroupCombos.push_back(groups);
  44                         }else {
  45                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  46                                         groups.push_back(globaldata->Groups[i]);
  47                                 }
  48                                 namesOfGroupCombos.push_back(groups);
  49                         }
  50                 }
  51
  52                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  53                         if(processors == 1){
  54                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  55                         }else{
  56                                 int numPairs = namesOfGroupCombos.size();
  57
  58                                 int numPairsPerProcessor = numPairs / processors;
  59
  60                                 for (int i = 0; i < processors; i++) {
  61                                         int startPos = i * numPairsPerProcessor;
  62
  63                                         if(i == processors - 1){
  64                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
  65                                         }
  66
  67                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
  68                                 }
  69                                 data = createProcesses(t, namesOfGroupCombos);
  70                                 lines.clear();
  71                         }
  72                 #else
  73                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  74                 #endif
  75
  76                 return data;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "Unweighted", "getValues");
  80                 exit(1);
  81         }
  82 }
  83 /**************************************************************************************************/
  84
  85 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
  86         try {
  87 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  88                 int process = 1;
  89                 vector<int> processIDS;
  90
  91                 EstOutput results;
  92
  93                 //loop through and create all the processes you want
  94                 while (process != processors) {
  95                         int pid = fork();
  96
  97                         if (pid > 0) {
  98                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
  99                                 process++;
 100                         }else if (pid == 0){
 101                                 EstOutput myresults;
 102                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
 103
 104                                 if (m->control_pressed) { exit(0); }
 105
 106                                 m->mothurOut("Merging results."); m->mothurOutEndLine();
 107
 108                                 //pass numSeqs to parent
 109                                 ofstream out;
 110                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 111                                 m->openOutputFile(tempFile, out);
 112                                 out << myresults.size() << endl;
 113                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 114                                 out.close();
 115
 116                                 exit(0);
 117                         }else {
 118                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 119                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 120                                 exit(0);
 121                         }
 122                 }
 123
 124                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
 125
 126                 //force parent to wait until all the processes are done
 127                 for (int i=0;i<(processors-1);i++) {
 128                         int temp = processIDS[i];
 129                         wait(&temp);
 130                 }
 131
 132                 if (m->control_pressed) { return results; }
 133
 134                 //get data created by processes
 135                 for (int i=0;i<(processors-1);i++) {
 136                         ifstream in;
 137                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 138                         m->openInputFile(s, in);
 139
 140                         //get quantiles
 141                         if (!in.eof()) {
 142                                 int num;
 143                                 in >> num; m->gobble(in);
 144
 145                                 if (m->control_pressed) { break; }
 146
 147                                 double w;
 148                                 for (int j = 0; j < num; j++) {
 149                                         in >> w;
 150                                         results.push_back(w);
 151                                 }
 152                                 m->gobble(in);
 153                         }
 154                         in.close();
 155                         remove(s.c_str());
 156                 }
 157
 158                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 159
 160                 return results;
 161 #endif
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "Unweighted", "createProcesses");
 165                 exit(1);
 166         }
 167 }
 168 /**************************************************************************************************/
 169 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
 170  try {
 171
 172
 173                 EstOutput results; results.resize(num);
 174
 175                 int count = 0;
 176                 int total = num;
 177                 int twentyPercent = (total * 0.20);
 178                 if (twentyPercent == 0) { twentyPercent = 1; }
 179
 180
 181                 for (int h = start; h < (start+num); h++) {
 182
 183                         if (m->control_pressed) { return results; }
 184
 185                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 186                         double totalBL = 0.00;  //all branch lengths
 187                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 188
 189                         //find a node that belongs to one of the groups in this combo
 190                         int nodeBelonging = -1;
 191                         for (int g = 0; g < namesOfGroupCombos[h].size(); g++) {
 192                                 if (t->groupNodeInfo[namesOfGroupCombos[h][g]].size() != 0) { nodeBelonging = t->groupNodeInfo[namesOfGroupCombos[h][g]][0]; break; }
 193                         }
 194
 195                         //sanity check
 196                         if (nodeBelonging == -1) {
 197                                 m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
 198                                 for (int g = 0; g < namesOfGroupCombos[h].size()-1; g++) { m->mothurOut(namesOfGroupCombos[h][g] + "-"); }
 199                                 m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
 200                                 m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
 201                         }else{
 202
 203                                 //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
 204                                 getRoot(t, nodeBelonging, namesOfGroupCombos[h]);
 205
 206                                 for(int i=0;i<t->getNumNodes();i++){
 207
 208                                         if (m->control_pressed) {  return data; }
 209
 210                                         //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 211                                         //pcountSize = 2, not unique to one group
 212                                         //pcountSize = 1, unique to one group
 213
 214                                         int pcountSize = 0;
 215                                         for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 216                                                 map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 217                                                 if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 218                                         }
 219
 220
 221                                         //unique calc
 222                                         if (pcountSize == 0) { }
 223                                         else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root
 224                                                 UniqueBL += abs(t->tree[i].getBranchLength());
 225                                         }
 226
 227                                         //total calc
 228                                         if (pcountSize == 0) { }
 229                                         else if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root
 230                                                 totalBL += abs(t->tree[i].getBranchLength());
 231                                         }
 232                                 }
 233         //cout << UniqueBL << '\t' << totalBL << endl;
 234                                 UW = (UniqueBL / totalBL);
 235
 236                                 if (isnan(UW) || isinf(UW)) { UW = 0; }
 237
 238                                 results[count] = UW;
 239                         }
 240                         count++;
 241
 242                         //report progress
 243                         //if((count % twentyPercent) == 0) {    float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
 244                 }
 245
 246                 //report progress
 247                 //if((count % twentyPercent) != 0) {    float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
 248
 249                 return results;
 250         }
 251         catch(exception& e) {
 252                 m->errorOut(e, "Unweighted", "driver");
 253                 exit(1);
 254         }
 255 }
 256 /**************************************************************************************************/
 257
 258 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
 259  try {
 260                 globaldata = GlobalData::getInstance();
 261                 processors = p;
 262                 outputDir = o;
 263
 264                 //if the users enters no groups then give them the score of all groups
 265                 int numGroups = globaldata->Groups.size();
 266
 267                 //calculate number of comparsions
 268                 int numComp = 0;
 269                 vector< vector<string> > namesOfGroupCombos;
 270                 for (int r=0; r<numGroups; r++) {
 271                         for (int l = 0; l < r; l++) {
 272                                 numComp++;
 273                                 vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
 274                                 namesOfGroupCombos.push_back(groups);
 275                         }
 276                 }
 277
 278                 if (numComp != 1) {
 279                         vector<string> groups;
 280                         if (numGroups == 0) {
 281                                 //get score for all users groups
 282                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 283                                         if (tmap->namesOfGroups[i] != "xxx") {
 284                                                 groups.push_back(tmap->namesOfGroups[i]);
 285                                         }
 286                                 }
 287                                 namesOfGroupCombos.push_back(groups);
 288                         }else {
 289                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 290                                         groups.push_back(globaldata->Groups[i]);
 291                                 }
 292                                 namesOfGroupCombos.push_back(groups);
 293                         }
 294                 }
 295
 296                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 297                         if(processors == 1){
 298                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 299                         }else{
 300                                 int numPairs = namesOfGroupCombos.size();
 301
 302                                 int numPairsPerProcessor = numPairs / processors;
 303
 304                                 for (int i = 0; i < processors; i++) {
 305                                         int startPos = i * numPairsPerProcessor;
 306                                         if(i == processors - 1){
 307                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
 308                                         }
 309                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
 310                                 }
 311
 312                                 data = createProcesses(t, namesOfGroupCombos, true);
 313
 314                                 lines.clear();
 315                         }
 316                 #else
 317                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 318                 #endif
 319
 320                 return data;
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "Unweighted", "getValues");
 324                 exit(1);
 325         }
 326 }
 327 /**************************************************************************************************/
 328
 329 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
 330         try {
 331 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 332                 int process = 1;
 333                 vector<int> processIDS;
 334
 335                 EstOutput results;
 336
 337                 //loop through and create all the processes you want
 338                 while (process != processors) {
 339                         int pid = fork();
 340
 341                         if (pid > 0) {
 342                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 343                                 process++;
 344                         }else if (pid == 0){
 345                                 EstOutput myresults;
 346                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
 347
 348                                 if (m->control_pressed) { exit(0); }
 349
 350                                 //pass numSeqs to parent
 351                                 ofstream out;
 352                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 353                                 m->openOutputFile(tempFile, out);
 354                                 out << myresults.size() << endl;
 355                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 356                                 out.close();
 357
 358                                 exit(0);
 359                         }else {
 360                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 361                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 362                                 exit(0);
 363                         }
 364                 }
 365
 366                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
 367
 368                 //force parent to wait until all the processes are done
 369                 for (int i=0;i<(processors-1);i++) {
 370                         int temp = processIDS[i];
 371                         wait(&temp);
 372                 }
 373
 374                 if (m->control_pressed) { return results; }
 375
 376                 //get data created by processes
 377                 for (int i=0;i<(processors-1);i++) {
 378                         ifstream in;
 379                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 380                         m->openInputFile(s, in);
 381
 382                         //get quantiles
 383                         if (!in.eof()) {
 384                                 int num;
 385                                 in >> num; m->gobble(in);
 386
 387                                 if (m->control_pressed) { break; }
 388
 389                                 double w;
 390                                 for (int j = 0; j < num; j++) {
 391                                         in >> w;
 392
 393                                         results.push_back(w);
 394                                 }
 395                                 m->gobble(in);
 396                         }
 397                         in.close();
 398                         remove(s.c_str());
 399                 }
 400
 401                 return results;
 402 #endif
 403         }
 404         catch(exception& e) {
 405                 m->errorOut(e, "Unweighted", "createProcesses");
 406                 exit(1);
 407         }
 408 }
 409 /**************************************************************************************************/
 410 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
 411  try {
 412
 413                 EstOutput results; results.resize(num);
 414
 415                 int count = 0;
 416
 417                 Tree* copyTree = new Tree;
 418
 419                 for (int h = start; h < (start+num); h++) {
 420
 421                         if (m->control_pressed) { return results; }
 422
 423                         //copy random tree passed in
 424                         copyTree->getCopy(t);
 425
 426                         //swap labels in the groups you want to compare
 427                         copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
 428
 429                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 430                         double totalBL = 0.00;  //all branch lengths
 431                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 432                         //find a node that belongs to one of the groups in this combo
 433                         int nodeBelonging = -1;
 434                         for (int g = 0; g < namesOfGroupCombos[h].size(); g++) {
 435                                 if (copyTree->groupNodeInfo[namesOfGroupCombos[h][g]].size() != 0) { nodeBelonging = copyTree->groupNodeInfo[namesOfGroupCombos[h][g]][0]; break; }
 436                         }
 437
 438                         //sanity check
 439                         if (nodeBelonging == -1) {
 440                                 m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
 441                                 for (int g = 0; g < namesOfGroupCombos[h].size()-1; g++) { m->mothurOut(namesOfGroupCombos[h][g] + "-"); }
 442                                 m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
 443                                 m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
 444                         }else{
 445
 446                                 //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
 447                                 getRoot(copyTree, nodeBelonging, namesOfGroupCombos[h]);
 448
 449                                 for(int i=0;i<copyTree->getNumNodes();i++){
 450
 451                                         if (m->control_pressed) {  return data; }
 452
 453                                         //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 454                                         //pcountSize = 2, not unique to one group
 455                                         //pcountSize = 1, unique to one group
 456
 457                                         int pcountSize = 0;
 458                                         for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 459                                                 map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 460                                                 if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 461                                         }
 462
 463                                         //unique calc
 464                                         if (pcountSize == 0) { }
 465                                         else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root
 466                                                 UniqueBL += abs(copyTree->tree[i].getBranchLength());
 467                                         }
 468
 469                                         //total calc
 470                                         if (pcountSize == 0) { }
 471                                         else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root
 472                                                 totalBL += abs(copyTree->tree[i].getBranchLength());
 473                                         }
 474
 475                                 }
 476                                 //cout << UniqueBL << '\t' << totalBL << endl;
 477                                 UW = (UniqueBL / totalBL);
 478
 479                                 if (isnan(UW) || isinf(UW)) { UW = 0; }
 480
 481                                 results[count] = UW;
 482                         }
 483                         count++;
 484
 485                 }
 486
 487                 delete copyTree;
 488
 489                 return results;
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "Unweighted", "driver");
 493                 exit(1);
 494         }
 495 }
 496 /**************************************************************************************************/
 497 int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) {
 498         try {
 499                 //you are a leaf so get your parent
 500                 int index = t->tree[index].getParent();
 501
 502                 if (includeRoot) {
 503                         rootForGrouping[grouping].clear();
 504                 }else {
 505                         //my parent is a potential root
 506                         rootForGrouping[grouping].insert(index);
 507
 508                         //while you aren't at root
 509                         while(t->tree[index].getParent() != -1){
 510
 511                                 if (m->control_pressed) {  return 0; }
 512
 513                                 //am I the root for this grouping? if so I want to stop "early"
 514                                 //does my sibling have descendants from the users groups?
 515                                 //if so I am not the root
 516                                 int parent = t->tree[index].getParent();
 517                                 int lc = t->tree[parent].getLChild();
 518                                 int rc = t->tree[parent].getRChild();
 519
 520                                 int sib = lc;
 521                                 if (lc == index) { sib = rc; }
 522
 523                                 map<string, int>::iterator itGroup;
 524                                 int pcountSize = 0;
 525                                 for (int j = 0; j < grouping.size(); j++) {
 526                                         map<string, int>::iterator itGroup = t->tree[sib].pcount.find(grouping[j]);
 527                                         if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 528                                 }
 529
 530                                 //if yes, I am not the root
 531                                 if (pcountSize != 0) {
 532                                         rootForGrouping[grouping].clear();
 533                                         rootForGrouping[grouping].insert(parent);
 534                                 }
 535
 536                                 index = parent;
 537                         }
 538
 539                         //get all nodes above the root to add so we don't add their u values above
 540                         index = *(rootForGrouping[grouping].begin());
 541                         while(t->tree[index].getParent() != -1){
 542                                 int parent = t->tree[index].getParent();
 543                                 rootForGrouping[grouping].insert(parent);
 544                                 //cout << parent << " in root" << endl;
 545                                 index = parent;
 546                         }
 547                 }
 548
 549                 return 0;
 550         }
 551         catch(exception& e) {
 552                 m->errorOut(e, "Unweighted", "getRoot");
 553                 exit(1);
 554         }
 555 }
 556 /**************************************************************************************************/
 557
 558