phylotree.cpp

   1 /*
   2  *  doTaxonomy.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 6/17/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "phylotree.h"
  11
  12 /**************************************************************************************************/
  13
  14 PhyloTree::PhyloTree(){
  15         try {
  16                 m = MothurOut::getInstance();
  17                 numNodes = 1;
  18                 numSeqs = 0;
  19                 tree.push_back(TaxNode("Root"));
  20                 tree[0].heirarchyID = "0";
  21                 maxLevel = 0;
  22                 calcTotals = true;
  23                 addSeqToTree("unknown", "unknown;");
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "PhyloTree", "PhyloTree");
  27                 exit(1);
  28         }
  29 }
  30 /**************************************************************************************************/
  31
  32 PhyloTree::PhyloTree(ifstream& in, string filename){
  33         try {
  34                 m = MothurOut::getInstance();
  35                 calcTotals = false;
  36                 numNodes = 0;
  37                 numSeqs = 0;
  38
  39                 #ifdef USE_MPI
  40                         MPI_File inMPI;
  41                         MPI_Offset size;
  42                         MPI_Status status;
  43
  44                         char inFileName[1024];
  45                         strcpy(inFileName, filename.c_str());
  46
  47                         MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
  48                         MPI_File_get_size(inMPI, &size);
  49
  50                         char* buffer = new char[size];
  51                         MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
  52
  53                         string tempBuf = buffer;
  54                         if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
  55                         istringstream iss (tempBuf,istringstream::in);
  56                         delete buffer;
  57
  58                         //read version
  59                         m->getline(iss); m->gobble(iss);
  60
  61                         iss >> numNodes; m->gobble(iss);
  62
  63                         tree.resize(numNodes);
  64
  65                         for (int i = 0; i < tree.size(); i++) {
  66                                 iss >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(iss);
  67                         }
  68
  69                         //read genus nodes
  70                         int numGenus = 0;
  71                         iss >> numGenus; m->gobble(iss);
  72
  73                         int gnode, gsize;
  74                         totals.clear();
  75                         for (int i = 0; i < numGenus; i++) {
  76                                 iss >> gnode >> gsize; m->gobble(iss);
  77
  78                                 uniqueTaxonomies[gnode] = gnode;
  79                                 totals.push_back(gsize);
  80                         }
  81
  82                         MPI_File_close(&inMPI);
  83
  84                 #else
  85                         //read version
  86                         string line = m->getline(in); m->gobble(in);
  87
  88                         in >> numNodes; m->gobble(in);
  89
  90                         tree.resize(numNodes);
  91
  92                         for (int i = 0; i < tree.size(); i++) {
  93                                 in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
  94                         }
  95
  96                         //read genus nodes
  97                         int numGenus = 0;
  98                         in >> numGenus; m->gobble(in);
  99
 100                         int gnode, gsize;
 101                         totals.clear();
 102                         for (int i = 0; i < numGenus; i++) {
 103                                 in >> gnode >> gsize; m->gobble(in);
 104
 105                                 uniqueTaxonomies[gnode] = gnode;
 106                                 totals.push_back(gsize);
 107                         }
 108
 109                         in.close();
 110
 111                 #endif
 112
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "PhyloTree", "PhyloTree");
 116                 exit(1);
 117         }
 118 }
 119 /**************************************************************************************************/
 120
 121 PhyloTree::PhyloTree(string tfile){
 122         try {
 123                 m = MothurOut::getInstance();
 124                 numNodes = 1;
 125                 numSeqs = 0;
 126                 tree.push_back(TaxNode("Root"));
 127                 tree[0].heirarchyID = "0";
 128                 maxLevel = 0;
 129                 calcTotals = true;
 130                 string name, tax;
 131
 132                 #ifdef USE_MPI
 133                         int pid, num, processors;
 134                         vector<unsigned long long> positions;
 135
 136                         MPI_Status status;
 137                         MPI_File inMPI;
 138                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 139                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 140
 141                         char inFileName[1024];
 142                         strcpy(inFileName, tfile.c_str());
 143
 144                         MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 145
 146                         if (pid == 0) {
 147                                 positions = m->setFilePosEachLine(tfile, num);
 148
 149                                 //send file positions to all processes
 150                                 for(int i = 1; i < processors; i++) {
 151                                         MPI_Send(&num, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 152                                         MPI_Send(&positions[0], (num+1), MPI_LONG, i, 2001, MPI_COMM_WORLD);
 153                                 }
 154                         }else{
 155                                 MPI_Recv(&num, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 156                                 positions.resize(num+1);
 157                                 MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, 2001, MPI_COMM_WORLD, &status);
 158                         }
 159
 160                         //read file
 161                         for(int i=0;i<num;i++){
 162                                 //read next sequence
 163                                 int length = positions[i+1] - positions[i];
 164                                 char* buf4 = new char[length];
 165
 166                                 MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
 167
 168                                 string tempBuf = buf4;
 169                                 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
 170                                 delete buf4;
 171
 172                                 istringstream iss (tempBuf,istringstream::in);
 173                                 iss >> name >> tax;
 174                                 addSeqToTree(name, tax);
 175                         }
 176
 177                         MPI_File_close(&inMPI);
 178                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 179
 180                 #else
 181                         ifstream in;
 182                         m->openInputFile(tfile, in);
 183
 184                         //read in users taxonomy file and add sequences to tree
 185                         while(!in.eof()){
 186                                 in >> name >> tax; m->gobble(in);
 187
 188                                 addSeqToTree(name, tax);
 189                         }
 190                         in.close();
 191                 #endif
 192
 193                 assignHeirarchyIDs(0);
 194
 195
 196         string unknownTax = "unknown;";
 197         //added last taxon until you get desired level
 198                 for (int i = 1; i < maxLevel; i++) {
 199                         unknownTax += "unclassfied;";
 200                 }
 201
 202         addSeqToTree("unknown", unknownTax);
 203
 204                 //create file for summary if needed
 205                 setUp(tfile);
 206         }
 207         catch(exception& e) {
 208                 m->errorOut(e, "PhyloTree", "PhyloTree");
 209                 exit(1);
 210         }
 211 }
 212
 213 /**************************************************************************************************/
 214
 215 string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 216         try {
 217                 string currentLevel = "";
 218                 if(heirarchy != ""){
 219                         int pos = heirarchy.find_first_of(';');
 220
 221                         if (pos == -1) { //you can't find another ;
 222                                 currentLevel = heirarchy;
 223                                 heirarchy = "";
 224                                 m->mothurOut(seqname + " is missing a ;, please check for other errors."); m->mothurOutEndLine();
 225                         }else{
 226                                 currentLevel=heirarchy.substr(0,pos);
 227                                 if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
 228                                 else { heirarchy = ""; }
 229                         }
 230
 231                 }
 232                 return currentLevel;
 233         }
 234         catch(exception& e) {
 235                 m->errorOut(e, "PhyloTree", "getNextTaxon");
 236                 exit(1);
 237         }
 238 }
 239
 240 /**************************************************************************************************/
 241
 242 int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 243         try {
 244                 numSeqs++;
 245
 246                 map<string, int>::iterator childPointer;
 247
 248                 int currentNode = 0;
 249                 int level = 1;
 250
 251                 tree[0].accessions.push_back(seqName);
 252                 m->removeConfidences(seqTaxonomy);
 253
 254                 string taxon;// = getNextTaxon(seqTaxonomy);
 255
 256                 while(seqTaxonomy != ""){
 257
 258                         level++;
 259
 260                         if (m->control_pressed) { return 0; }
 261
 262                         //somehow the parent is getting one too many accnos
 263                         //use print to reassign the taxa id
 264                         taxon = getNextTaxon(seqTaxonomy, seqName);
 265
 266                         if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies[currentNode] = currentNode; } break;  }
 267
 268                         childPointer = tree[currentNode].children.find(taxon);
 269
 270                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, move on
 271                                 currentNode = childPointer->second;
 272                                 tree[currentNode].accessions.push_back(seqName);
 273                                 name2Taxonomy[seqName] = currentNode;
 274                         }
 275                         else{                                                                                   //otherwise, create it
 276                                 tree.push_back(TaxNode(taxon));
 277                                 numNodes++;
 278                                 tree[currentNode].children[taxon] = numNodes-1;
 279                                 tree[numNodes-1].parent = currentNode;
 280
 281                                 currentNode = tree[currentNode].children[taxon];
 282                                 tree[currentNode].accessions.push_back(seqName);
 283                                 name2Taxonomy[seqName] = currentNode;
 284                         }
 285
 286                         if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode; }
 287                 }
 288
 289                 return 0;
 290         }
 291         catch(exception& e) {
 292                 m->errorOut(e, "PhyloTree", "addSeqToTree");
 293                 exit(1);
 294         }
 295 }
 296 /**************************************************************************************************/
 297 vector<int> PhyloTree::getGenusNodes()  {
 298         try {
 299                 genusIndex.clear();
 300                 //generate genusIndexes
 301                 map<int, int>::iterator it2;
 302                 for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  genusIndex.push_back(it2->first);     }
 303
 304                 return genusIndex;
 305         }
 306         catch(exception& e) {
 307                 m->errorOut(e, "PhyloTree", "getGenusNodes");
 308                 exit(1);
 309         }
 310 }
 311 /**************************************************************************************************/
 312 vector<int> PhyloTree::getGenusTotals() {
 313         try {
 314
 315                 if (calcTotals) {
 316                         totals.clear();
 317                         //reset counts because we are on a new word
 318                         for (int j = 0; j < genusIndex.size(); j++) {
 319                                 totals.push_back(tree[genusIndex[j]].accessions.size());
 320                         }
 321                         return totals;
 322                 }else{
 323                         return totals;
 324                 }
 325
 326         }
 327         catch(exception& e) {
 328                 m->errorOut(e, "PhyloTree", "getGenusNodes");
 329                 exit(1);
 330         }
 331 }
 332 /**************************************************************************************************/
 333
 334 void PhyloTree::assignHeirarchyIDs(int index){
 335         try {
 336                 map<string,int>::iterator it;
 337                 int counter = 1;
 338
 339                 for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
 340                         tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
 341                         counter++;
 342                         tree[it->second].level = tree[index].level + 1;
 343
 344                         //save maxLevel for binning the unclassified seqs
 345                         if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; }
 346
 347                         assignHeirarchyIDs(it->second);
 348                 }
 349         }
 350         catch(exception& e) {
 351                 m->errorOut(e, "PhyloTree", "assignHeirarchyIDs");
 352                 exit(1);
 353         }
 354 }
 355 /**************************************************************************************************/
 356 void PhyloTree::setUp(string tfile){
 357         try{
 358                 string taxFileNameTest = tfile.substr(0,tfile.find_last_of(".")+1) + "tree.sum";
 359
 360                 #ifdef USE_MPI
 361                         int pid;
 362                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 363
 364                         if (pid == 0) {  binUnclassified(taxFileNameTest);  }
 365
 366                 #else
 367                         binUnclassified(taxFileNameTest);
 368                 #endif
 369         }
 370         catch(exception& e) {
 371                 m->errorOut(e, "PhyloTree", "setUp");
 372                 exit(1);
 373         }
 374 }
 375 /**************************************************************************************************/
 376 void PhyloTree::binUnclassified(string file){
 377         try {
 378
 379                 ofstream out;
 380                 m->openOutputFile(file, out);
 381
 382                 map<string, int>::iterator itBin;
 383                 map<string, int>::iterator childPointer;
 384
 385                 vector<TaxNode> copy = tree;
 386
 387                 //fill out tree
 388                 fillOutTree(0, copy);
 389
 390                 //get leaf nodes that may need extension
 391                 for (int i = 0; i < copy.size(); i++) {
 392
 393                         if (copy[i].children.size() == 0) {
 394                                 leafNodes[i] = i;
 395                         }
 396                 }
 397
 398                 int copyNodes = copy.size();
 399
 400                 //go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
 401                 map<int, int>::iterator itLeaf;
 402                 for (itLeaf = leafNodes.begin(); itLeaf != leafNodes.end(); itLeaf++) {
 403
 404                         if (m->control_pressed) {  out.close(); break;  }
 405
 406                         int level = copy[itLeaf->second].level;
 407                         int currentNode = itLeaf->second;
 408
 409                         //this sequence is unclassified at some levels
 410                         while(level < maxLevel){
 411
 412                                 level++;
 413
 414                                 string taxon = "unclassified";
 415
 416                                 //does the parent have a child names 'unclassified'?
 417                                 childPointer = copy[currentNode].children.find(taxon);
 418
 419                                 if(childPointer != copy[currentNode].children.end()){   //if the node already exists, move on
 420                                         currentNode = childPointer->second; //currentNode becomes 'unclassified'
 421                                 }
 422                                 else{                                                                                   //otherwise, create it
 423                                         copy.push_back(TaxNode(taxon));
 424                                         copyNodes++;
 425                                         copy[currentNode].children[taxon] = copyNodes-1;
 426                                         copy[copyNodes-1].parent = currentNode;
 427                                         copy[copyNodes-1].level = copy[currentNode].level + 1;
 428
 429                                         currentNode = copy[currentNode].children[taxon];
 430                                 }
 431                         }
 432                 }
 433
 434                 if (!m->control_pressed) {
 435                         //print copy tree
 436                         print(out, copy);
 437                 }
 438
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "PhyloTree", "binUnclassified");
 442                 exit(1);
 443         }
 444 }
 445 /**************************************************************************************************/
 446 void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
 447         try {
 448
 449                 map<string,int>::iterator it;
 450
 451                 it = copy[index].children.find("unclassified");
 452                 if (it == copy[index].children.end()) { //no unclassified at this level
 453                         string taxon = "unclassified";
 454                         copy.push_back(TaxNode(taxon));
 455                         copy[index].children[taxon] = copy.size()-1;
 456                         copy[copy.size()-1].parent = index;
 457                         copy[copy.size()-1].level = copy[index].level + 1;
 458                 }
 459
 460                 if (tree[index].level < maxLevel) {
 461                         for(it=tree[index].children.begin();it!=tree[index].children.end();it++){ //check your children
 462                                 fillOutTree(it->second, copy);
 463                         }
 464                 }
 465
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "PhyloTree", "fillOutTree");
 469                 exit(1);
 470         }
 471 }
 472 /**************************************************************************************************/
 473 string PhyloTree::getFullTaxonomy(string seqName) {
 474         try {
 475                 string tax = "";
 476
 477                 int currentNode = name2Taxonomy[seqName];
 478
 479                 while (tree[currentNode].parent != -1) {
 480                         tax = tree[currentNode].name + ";" + tax;
 481                         currentNode = tree[currentNode].parent;
 482                 }
 483
 484                 return tax;
 485         }
 486         catch(exception& e) {
 487                 m->errorOut(e, "PhyloTree", "getFullTaxonomy");
 488                 exit(1);
 489         }
 490 }
 491 /**************************************************************************************************/
 492
 493 void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
 494         try {
 495
 496                 //output mothur version
 497                 out << "#" << m->getVersion() << endl;
 498
 499                 out << copy.size() << endl;
 500
 501                 out << maxLevel << endl;
 502
 503                 for (int i = 0; i < copy.size(); i++) {
 504
 505                         out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size() << '\t';
 506
 507                         map<string,int>::iterator it;
 508                         for(it=copy[i].children.begin();it!=copy[i].children.end();it++){
 509                                 out << it->first << '\t' << it->second << '\t';
 510                         }
 511                         out << endl;
 512                 }
 513
 514                 out.close();
 515         }
 516         catch(exception& e) {
 517                 m->errorOut(e, "PhyloTree", "print");
 518                 exit(1);
 519         }
 520 }
 521 /**************************************************************************************************/
 522 void PhyloTree::printTreeNodes(string treefilename) {
 523         try {
 524
 525                 #ifdef USE_MPI
 526                         int pid;
 527                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 528
 529                         if (pid == 0) {
 530
 531                 #endif
 532
 533                         ofstream outTree;
 534                         m->openOutputFile(treefilename, outTree);
 535
 536                         //output mothur version
 537                         outTree << "#" << m->getVersion() << endl;
 538
 539                         //print treenodes
 540                         outTree << tree.size() << endl;
 541                         for (int i = 0; i < tree.size(); i++) {
 542                                 outTree << tree[i].name << '\t' << tree[i].level << '\t' << tree[i].parent << endl;
 543                         }
 544
 545                         //print genus nodes
 546                         outTree << endl << uniqueTaxonomies.size() << endl;
 547                         map<int, int>::iterator it2;
 548                         for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  outTree << it2->first << '\t' << tree[it2->first].accessions.size() << endl;  }
 549                         outTree << endl;
 550
 551                         outTree.close();
 552
 553                 #ifdef USE_MPI
 554                         }
 555                 #endif
 556
 557
 558         }
 559         catch(exception& e) {
 560                 m->errorOut(e, "PhyloTree", "printTreeNodes");
 561                 exit(1);
 562         }
 563 }
 564 /**************************************************************************************************/
 565 TaxNode PhyloTree::get(int i ){
 566         try {
 567                 if (i < tree.size()) {  return tree[i];  }
 568                 else {  cout << i << '\t' << tree.size() << endl ; m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
 569         }
 570         catch(exception& e) {
 571                 m->errorOut(e, "PhyloTree", "get");
 572                 exit(1);
 573         }
 574 }
 575 /**************************************************************************************************/
 576 TaxNode PhyloTree::get(string seqName){
 577         try {
 578                 map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
 579
 580                 if (itFind != name2Taxonomy.end()) {  return tree[name2Taxonomy[seqName]];  }
 581                 else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
 582         }
 583         catch(exception& e) {
 584                 m->errorOut(e, "PhyloTree", "get");
 585                 exit(1);
 586         }
 587 }
 588 /**************************************************************************************************/
 589 string PhyloTree::getName(int i ){
 590         try {
 591                 if (i < tree.size()) {  return tree[i].name;     }
 592                 else { m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
 593         }
 594         catch(exception& e) {
 595                 m->errorOut(e, "PhyloTree", "get");
 596                 exit(1);
 597         }
 598 }
 599 /**************************************************************************************************/
 600 int PhyloTree::getIndex(string seqName){
 601         try {
 602                 map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
 603
 604                 if (itFind != name2Taxonomy.end()) {  return name2Taxonomy[seqName];  }
 605                 else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
 606         }
 607         catch(exception& e) {
 608                 m->errorOut(e, "PhyloTree", "get");
 609                 exit(1);
 610         }
 611 }
 612 /**************************************************************************************************/
 613 bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
 614         try {
 615
 616                 bool okay = true;
 617                 templateFileNames.push_back("unknown");
 618
 619                 map<string, int>::iterator itFind;
 620                 map<string, int> taxonomyFileNames = name2Taxonomy;
 621
 622         if (m->debug) { m->mothurOut("[DEBUG]: in error check. Numseqs in template = " + toString(templateFileNames.size()) + ". Numseqs in taxonomy = " + toString(taxonomyFileNames.size()) + ".\n"); }
 623
 624                 for (int i = 0; i < templateFileNames.size(); i++) {
 625                         itFind = taxonomyFileNames.find(templateFileNames[i]);
 626
 627                         if (itFind != taxonomyFileNames.end()) { //found it so erase it
 628                                 taxonomyFileNames.erase(itFind);
 629                         }else {
 630                                 m->mothurOut("'" +templateFileNames[i] + "' is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
 631                                 okay = false;
 632                         }
 633
 634                         //templateFileNames.erase(templateFileNames.begin()+i);
 635                         //i--;
 636                 }
 637                 templateFileNames.clear();
 638
 639                 if (taxonomyFileNames.size() > 0) { //there are names in tax file that are not in template
 640                         okay = false;
 641
 642                         for (itFind = taxonomyFileNames.begin(); itFind != taxonomyFileNames.end(); itFind++) {
 643                                 m->mothurOut(itFind->first + " is in your taxonomy file and is not in your template file. Please correct."); m->mothurOutEndLine();
 644                         }
 645                 }
 646
 647                 return okay;
 648         }
 649         catch(exception& e) {
 650                 m->errorOut(e, "PhyloTree", "ErrorCheck");
 651                 exit(1);
 652         }
 653 }
 654 /**************************************************************************************************/
 655
 656
 657
 658