phylosummary.cpp

   1 /*
   2  *  rawTrainingDataMaker.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 4/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "phylosummary.h"
  11
  12 /**************************************************************************************************/
  13
  14 PhyloSummary::PhyloSummary(string refTfile, string groupFile){
  15         try {
  16                 m = MothurOut::getInstance();
  17                 maxLevel = 0;
  18                 ignore = false;
  19
  20                 if (groupFile != "") {
  21                         groupmap = new GroupMap(groupFile);
  22                         groupmap->readMap();
  23                 }else{
  24                         groupmap = NULL;
  25                 }
  26
  27                 //check for necessary files
  28                 string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
  29                 ifstream FileTest(taxFileNameTest.c_str());
  30
  31                 if (!FileTest) {
  32                         m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
  33                 }else{
  34                         readTreeStruct(FileTest);
  35                 }
  36
  37                 tree[0].rank = "0";
  38                 assignRank(0);
  39
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "PhyloSummary", "PhyloSummary");
  43                 exit(1);
  44         }
  45 }
  46
  47 /**************************************************************************************************/
  48
  49 PhyloSummary::PhyloSummary(string groupFile){
  50         try {
  51                 m = MothurOut::getInstance();
  52                 maxLevel = 0;
  53                 ignore = true;
  54
  55                 if (groupFile != "") {
  56                         groupmap = new GroupMap(groupFile);
  57                         groupmap->readMap();
  58                 }else{
  59                         groupmap = NULL;
  60                 }
  61
  62                 tree.push_back(rawTaxNode("Root"));
  63                 tree[0].rank = "0";
  64
  65
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "PhyloSummary", "PhyloSummary");
  69                 exit(1);
  70         }
  71 }
  72 /**************************************************************************************************/
  73
  74 int PhyloSummary::summarize(string userTfile){
  75         try {
  76
  77                 ifstream in;
  78                 m->openInputFile(userTfile, in);
  79
  80                 //read in users taxonomy file and add sequences to tree
  81                 string name, tax;
  82                 int numSeqs = 0;
  83                 while(!in.eof()){
  84                         in >> name >> tax; m->gobble(in);
  85
  86                         addSeqToTree(name, tax);
  87                         numSeqs++;
  88
  89                         if (m->control_pressed) { break;  }
  90                 }
  91                 in.close();
  92
  93                 return numSeqs;
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "PhyloSummary", "summarize");
  97                 exit(1);
  98         }
  99 }
 100
 101 /**************************************************************************************************/
 102
 103 string PhyloSummary::getNextTaxon(string& heirarchy){
 104         try {
 105                 string currentLevel = "";
 106                 if(heirarchy != ""){
 107                         int pos = heirarchy.find_first_of(';');
 108                         currentLevel=heirarchy.substr(0,pos);
 109                         if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
 110                         else { heirarchy = ""; }
 111                 }
 112                 return currentLevel;
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "PhyloSummary", "getNextTaxon");
 116                 exit(1);
 117         }
 118 }
 119
 120 /**************************************************************************************************/
 121
 122 int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 123         try {
 124
 125                 numSeqs++;
 126
 127                 map<string, int>::iterator childPointer;
 128
 129                 int currentNode = 0;
 130                 string taxon;
 131
 132                 int level = 0;
 133
 134                 //are there confidence scores, if so remove them
 135                 if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy); }
 136
 137                 while (seqTaxonomy != "") {
 138
 139                         if (m->control_pressed) { return 0; }
 140
 141                         //somehow the parent is getting one too many accnos
 142                         //use print to reassign the taxa id
 143                         taxon = getNextTaxon(seqTaxonomy);
 144
 145                         childPointer = tree[currentNode].children.find(taxon);
 146
 147                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, update count and move on
 148                                 if (groupmap != NULL) {
 149                                         //find out the sequences group
 150                                         string group = groupmap->getGroup(seqName);
 151
 152                                         if (group == "not found") {  m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 153
 154                                         //do you have a count for this group?
 155                                         map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(group);
 156
 157                                         //if yes, increment it - there should not be a case where we can't find it since we load group in read
 158                                         if (itGroup != tree[childPointer->second].groupCount.end()) {
 159                                                 tree[childPointer->second].groupCount[group]++;
 160                                         }
 161                                 }
 162
 163                                 tree[childPointer->second].total++;
 164
 165                                 currentNode = childPointer->second;
 166                         }else{
 167                                 if (ignore) {
 168
 169                                         tree.push_back(rawTaxNode(taxon));
 170                                         int index = tree.size() - 1;
 171
 172                                         tree[index].parent = currentNode;
 173                                         tree[index].level = (level+1);
 174                                         tree[index].total = 1;
 175                                         tree[currentNode].children[taxon] = index;
 176
 177                                         //initialize groupcounts
 178                                         if (groupmap != NULL) {
 179                                                 vector<string> mGroups = groupmap->getNamesOfGroups();
 180                                                 for (int j = 0; j < mGroups.size(); j++) {
 181                                                         tree[index].groupCount[mGroups[j]] = 0;
 182                                                 }
 183
 184                                                 //find out the sequences group
 185                                                 string group = groupmap->getGroup(seqName);
 186
 187                                                 if (group == "not found") {  m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 188
 189                                                 //do you have a count for this group?
 190                                                 map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
 191
 192                                                 //if yes, increment it - there should not be a case where we can't find it since we load group in read
 193                                                 if (itGroup != tree[index].groupCount.end()) {
 194                                                         tree[index].groupCount[group]++;
 195                                                 }
 196                                         }
 197
 198                                         currentNode = index;
 199
 200                                 }else{ //otherwise, error
 201                                         m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
 202                                         break;
 203                                 }
 204                         }
 205
 206                         level++;
 207
 208                         if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
 209                                 for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
 210                         }
 211                 }
 212                 return 0;
 213         }
 214         catch(exception& e) {
 215                 m->errorOut(e, "PhyloSummary", "addSeqToTree");
 216                 exit(1);
 217         }
 218 }
 219 /**************************************************************************************************/
 220
 221 int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 222         try {
 223                 numSeqs++;
 224
 225                 map<string, int>::iterator childPointer;
 226
 227                 int currentNode = 0;
 228                 string taxon;
 229
 230                 int level = 0;
 231
 232                 //are there confidence scores, if so remove them
 233                 if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy); }
 234
 235                 while (seqTaxonomy != "") {
 236
 237                         if (m->control_pressed) { return 0; }
 238
 239                         //somehow the parent is getting one too many accnos
 240                         //use print to reassign the taxa id
 241                         taxon = getNextTaxon(seqTaxonomy);
 242
 243                         childPointer = tree[currentNode].children.find(taxon);
 244
 245                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, update count and move on
 246                                 if (groupmap != NULL) {
 247
 248                                         map<string, bool> containsGroup;
 249                                         vector<string> mGroups = groupmap->getNamesOfGroups();
 250                                         for (int j = 0; j < mGroups.size(); j++) {
 251                                                 containsGroup[mGroups[j]] = false;
 252                                         }
 253
 254                                         for (int k = 0; k < names.size(); k++) {
 255                                                 //find out the sequences group
 256                                                 string group = groupmap->getGroup(names[k]);
 257
 258                                                 if (group == "not found") {  m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 259                                                 else {
 260                                                         containsGroup[group] = true;
 261                                                 }
 262                                         }
 263
 264                                         for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
 265                                                 if (itGroup->second == true) {
 266                                                         tree[childPointer->second].groupCount[itGroup->first]++;
 267                                                 }
 268                                         }
 269
 270                                 }
 271
 272                                 tree[childPointer->second].total++;
 273
 274                                 currentNode = childPointer->second;
 275                         }else{
 276                                 if (ignore) {
 277
 278                                         tree.push_back(rawTaxNode(taxon));
 279                                         int index = tree.size() - 1;
 280
 281                                         tree[index].parent = currentNode;
 282                                         tree[index].level = (level+1);
 283                                         tree[index].total = 1;
 284                                         tree[currentNode].children[taxon] = index;
 285
 286                                         //initialize groupcounts
 287                                         if (groupmap != NULL) {
 288                                                 map<string, bool> containsGroup;
 289                                                 vector<string> mGroups = groupmap->getNamesOfGroups();
 290                                                 for (int j = 0; j < mGroups.size(); j++) {
 291                                                         tree[index].groupCount[mGroups[j]] = 0;
 292                                                         containsGroup[mGroups[j]] = false;
 293                                                 }
 294
 295
 296                                                 for (int k = 0; k < names.size(); k++) {
 297                                                         //find out the sequences group
 298                                                         string group = groupmap->getGroup(names[k]);
 299
 300                                                         if (group == "not found") {  m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 301                                                         else {
 302                                                                 containsGroup[group] = true;
 303                                                         }
 304                                                 }
 305
 306                                                 for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
 307                                                         if (itGroup->second == true) {
 308                                                                 tree[index].groupCount[itGroup->first]++;
 309                                                         }
 310                                                 }
 311                                         }
 312
 313                                         currentNode = index;
 314
 315                                 }else{ //otherwise, error
 316                                         m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
 317                                         break;
 318                                 }
 319                         }
 320
 321                         level++;
 322
 323                         if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
 324                                 for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
 325                         }
 326                 }
 327                 return 0;
 328         }
 329         catch(exception& e) {
 330                 m->errorOut(e, "PhyloSummary", "addSeqToTree");
 331                 exit(1);
 332         }
 333 }
 334
 335 /**************************************************************************************************/
 336
 337 void PhyloSummary::assignRank(int index){
 338         try {
 339                 map<string,int>::iterator it;
 340                 int counter = 1;
 341
 342                 for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
 343                         tree[it->second].rank = tree[index].rank + '.' + toString(counter);
 344                         counter++;
 345
 346                         assignRank(it->second);
 347                 }
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "PhyloSummary", "assignRank");
 351                 exit(1);
 352         }
 353 }
 354 /**************************************************************************************************/
 355
 356 void PhyloSummary::print(ofstream& out){
 357         try {
 358
 359                 if (ignore) { assignRank(0); }
 360
 361                 //print labels
 362                 out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
 363                 if (groupmap != NULL) {
 364                         //so the labels match the counts below, since the map sorts them automatically...
 365                         //sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
 366                         vector<string> mGroups = groupmap->getNamesOfGroups();
 367                         for (int i = 0; i < mGroups.size(); i++) {
 368                                 out << mGroups[i] << '\t';
 369                         }
 370                 }
 371
 372                 out << endl;
 373
 374                 int totalChildrenInTree = 0;
 375                 map<string, int>::iterator itGroup;
 376
 377                 map<string,int>::iterator it;
 378                 for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
 379                         if (tree[it->second].total != 0)  {
 380                                 totalChildrenInTree++;
 381                                 tree[0].total += tree[it->second].total;
 382
 383                                 if (groupmap != NULL) {
 384                                         vector<string> mGroups = groupmap->getNamesOfGroups();
 385                                         for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; }
 386                                 }
 387                         }
 388                 }
 389
 390                 //print root
 391                 out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
 392
 393
 394                 if (groupmap != NULL) {
 395                         //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
 396                         //      out << itGroup->second << '\t';
 397                         //}
 398                         vector<string> mGroups = groupmap->getNamesOfGroups();
 399                         for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; }
 400                 }
 401                 out << endl;
 402
 403                 //print rest
 404                 print(0, out);
 405
 406         }
 407         catch(exception& e) {
 408                 m->errorOut(e, "PhyloSummary", "print");
 409                 exit(1);
 410         }
 411 }
 412
 413 /**************************************************************************************************/
 414
 415 void PhyloSummary::print(int i, ofstream& out){
 416         try {
 417                 map<string,int>::iterator it;
 418                 for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
 419
 420                         if (tree[it->second].total != 0)  {
 421
 422                                 int totalChildrenInTree = 0;
 423
 424                                 map<string,int>::iterator it2;
 425                                 for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
 426                                         if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
 427                                 }
 428
 429                                 out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
 430
 431                                 map<string, int>::iterator itGroup;
 432                                 if (groupmap != NULL) {
 433                                         //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
 434                                         //      out << itGroup->second << '\t';
 435                                         //}
 436                                         vector<string> mGroups = groupmap->getNamesOfGroups();
 437                                         for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
 438                                 }
 439                                 out << endl;
 440
 441                         }
 442
 443                         print(it->second, out);
 444                 }
 445         }
 446         catch(exception& e) {
 447                 m->errorOut(e, "PhyloSummary", "print");
 448                 exit(1);
 449         }
 450 }
 451 /**************************************************************************************************/
 452 void PhyloSummary::readTreeStruct(ifstream& in){
 453         try {
 454
 455                 //read version
 456                 string line = m->getline(in); m->gobble(in);
 457
 458                 int num;
 459
 460                 in >> num; m->gobble(in);
 461
 462                 tree.resize(num);
 463
 464                 in >> maxLevel; m->gobble(in);
 465
 466                 //read the tree file
 467                 for (int i = 0; i < tree.size(); i++) {
 468
 469                         in >> tree[i].level >> tree[i].name >> num; //num contains the number of children tree[i] has
 470
 471                         //set children
 472                         string childName;
 473                         int childIndex;
 474                         for (int j = 0; j < num; j++) {
 475                                 in >> childName >> childIndex;
 476                                 tree[i].children[childName] = childIndex;
 477                         }
 478
 479                         //initialize groupcounts
 480                         if (groupmap != NULL) {
 481                                 for (int j = 0; j < (groupmap->getNamesOfGroups()).size(); j++) {
 482                                         tree[i].groupCount[(groupmap->getNamesOfGroups())[j]] = 0;
 483                                 }
 484                         }
 485
 486                         tree[i].total = 0;
 487
 488                         m->gobble(in);
 489
 490                         //if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
 491                 }
 492
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "PhyloSummary", "readTreeStruct");
 496                 exit(1);
 497         }
 498 }
 499 /**************************************************************************************************/
 500
 501
 502