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 = 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 void 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                 while(!in.eof()){
  83                         in >> name >> tax; m->gobble(in);
  84
  85                         addSeqToTree(name, tax);
  86
  87                         if (m->control_pressed) { break;  }
  88                 }
  89                 in.close();
  90         }
  91         catch(exception& e) {
  92                 m->errorOut(e, "PhyloSummary", "summarize");
  93                 exit(1);
  94         }
  95 }
  96
  97 /**************************************************************************************************/
  98
  99 string PhyloSummary::getNextTaxon(string& heirarchy){
 100         try {
 101                 string currentLevel = "";
 102                 if(heirarchy != ""){
 103                         int pos = heirarchy.find_first_of(';');
 104                         currentLevel=heirarchy.substr(0,pos);
 105                         if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
 106                         else { heirarchy = ""; }
 107                 }
 108                 return currentLevel;
 109         }
 110         catch(exception& e) {
 111                 m->errorOut(e, "PhyloSummary", "getNextTaxon");
 112                 exit(1);
 113         }
 114 }
 115
 116 /**************************************************************************************************/
 117
 118 int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 119         try {
 120                 numSeqs++;
 121
 122                 map<string, int>::iterator childPointer;
 123
 124                 int currentNode = 0;
 125                 string taxon;
 126
 127                 int level = 0;
 128
 129                 while (seqTaxonomy != "") {
 130
 131                         if (m->control_pressed) { return 0; }
 132
 133                         //somehow the parent is getting one too many accnos
 134                         //use print to reassign the taxa id
 135                         taxon = getNextTaxon(seqTaxonomy);
 136
 137                         childPointer = tree[currentNode].children.find(taxon);
 138
 139                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, update count and move on
 140                                 if (groupmap != NULL) {
 141                                         //find out the sequences group
 142                                         string group = groupmap->getGroup(seqName);
 143
 144                                         if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 145
 146                                         //do you have a count for this group?
 147                                         map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(group);
 148
 149                                         //if yes, increment it - there should not be a case where we can't find it since we load group in read
 150                                         if (itGroup != tree[childPointer->second].groupCount.end()) {
 151                                                 tree[childPointer->second].groupCount[group]++;
 152                                         }
 153                                 }
 154
 155                                 tree[childPointer->second].total++;
 156
 157                                 currentNode = childPointer->second;
 158                         }else{
 159                                 if (ignore) {
 160
 161                                         tree.push_back(rawTaxNode(taxon));
 162                                         int index = tree.size() - 1;
 163
 164                                         tree[index].parent = currentNode;
 165                                         tree[index].level = (level+1);
 166                                         tree[index].total = 1;
 167                                         tree[currentNode].children[taxon] = index;
 168
 169                                         //initialize groupcounts
 170                                         if (groupmap != NULL) {
 171                                                 for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
 172                                                         tree[index].groupCount[groupmap->namesOfGroups[j]] = 0;
 173                                                 }
 174
 175                                                 //find out the sequences group
 176                                                 string group = groupmap->getGroup(seqName);
 177
 178                                                 if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 179
 180                                                 //do you have a count for this group?
 181                                                 map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
 182
 183                                                 //if yes, increment it - there should not be a case where we can't find it since we load group in read
 184                                                 if (itGroup != tree[index].groupCount.end()) {
 185                                                         tree[index].groupCount[group]++;
 186                                                 }
 187                                         }
 188
 189                                         currentNode = index;
 190
 191                                 }else{ //otherwise, error
 192                                         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();
 193                                         break;
 194                                 }
 195                         }
 196
 197                         level++;
 198
 199                         if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
 200                                 for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
 201                         }
 202                 }
 203                 return 0;
 204         }
 205         catch(exception& e) {
 206                 m->errorOut(e, "PhyloSummary", "addSeqToTree");
 207                 exit(1);
 208         }
 209 }
 210 /**************************************************************************************************/
 211
 212 int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 213         try {
 214                 numSeqs++;
 215
 216                 map<string, int>::iterator childPointer;
 217
 218                 int currentNode = 0;
 219                 string taxon;
 220
 221                 int level = 0;
 222
 223                 while (seqTaxonomy != "") {
 224
 225                         if (m->control_pressed) { return 0; }
 226
 227                         //somehow the parent is getting one too many accnos
 228                         //use print to reassign the taxa id
 229                         taxon = getNextTaxon(seqTaxonomy);
 230
 231                         childPointer = tree[currentNode].children.find(taxon);
 232
 233                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, update count and move on
 234                                 if (groupmap != NULL) {
 235
 236                                         map<string, bool> containsGroup;
 237                                         for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
 238                                                 containsGroup[groupmap->namesOfGroups[j]] = false;
 239                                         }
 240
 241                                         for (int k = 0; k < names.size(); k++) {
 242                                                 //find out the sequences group
 243                                                 string group = groupmap->getGroup(names[k]);
 244
 245                                                 if (group == "not found") {  m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 246                                                 else {
 247                                                         containsGroup[group] = true;
 248                                                 }
 249                                         }
 250
 251                                         for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
 252                                                 if (itGroup->second == true) {
 253                                                         tree[childPointer->second].groupCount[itGroup->first]++;
 254                                                 }
 255                                         }
 256
 257                                 }
 258
 259                                 tree[childPointer->second].total++;
 260
 261                                 currentNode = childPointer->second;
 262                         }else{
 263                                 if (ignore) {
 264
 265                                         tree.push_back(rawTaxNode(taxon));
 266                                         int index = tree.size() - 1;
 267
 268                                         tree[index].parent = currentNode;
 269                                         tree[index].level = (level+1);
 270                                         tree[index].total = 1;
 271                                         tree[currentNode].children[taxon] = index;
 272
 273                                         //initialize groupcounts
 274                                         if (groupmap != NULL) {
 275                                                 map<string, bool> containsGroup;
 276                                                 for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
 277                                                         tree[index].groupCount[groupmap->namesOfGroups[j]] = 0;
 278                                                         containsGroup[groupmap->namesOfGroups[j]] = false;
 279                                                 }
 280
 281
 282                                                 for (int k = 0; k < names.size(); k++) {
 283                                                         //find out the sequences group
 284                                                         string group = groupmap->getGroup(names[k]);
 285
 286                                                         if (group == "not found") {  m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 287                                                         else {
 288                                                                 containsGroup[group] = true;
 289                                                         }
 290                                                 }
 291
 292                                                 for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
 293                                                         if (itGroup->second == true) {
 294                                                                 tree[index].groupCount[itGroup->first]++;
 295                                                         }
 296                                                 }
 297                                         }
 298
 299                                         currentNode = index;
 300
 301                                 }else{ //otherwise, error
 302                                         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();
 303                                         break;
 304                                 }
 305                         }
 306
 307                         level++;
 308
 309                         if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
 310                                 for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
 311                         }
 312                 }
 313                 return 0;
 314         }
 315         catch(exception& e) {
 316                 m->errorOut(e, "PhyloSummary", "addSeqToTree");
 317                 exit(1);
 318         }
 319 }
 320
 321 /**************************************************************************************************/
 322
 323 void PhyloSummary::assignRank(int index){
 324         try {
 325                 map<string,int>::iterator it;
 326                 int counter = 1;
 327
 328                 for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
 329                         tree[it->second].rank = tree[index].rank + '.' + toString(counter);
 330                         counter++;
 331
 332                         assignRank(it->second);
 333                 }
 334         }
 335         catch(exception& e) {
 336                 m->errorOut(e, "PhyloSummary", "assignRank");
 337                 exit(1);
 338         }
 339 }
 340 /**************************************************************************************************/
 341
 342 void PhyloSummary::print(ofstream& out){
 343         try {
 344
 345                 if (ignore) { assignRank(0); }
 346
 347                 //print labels
 348                 out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
 349                 if (groupmap != NULL) {
 350                         //so the labels match the counts below, since the map sorts them automatically...
 351                         //sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
 352
 353                         for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
 354                                 out << groupmap->namesOfGroups[i] << '\t';
 355                         }
 356                 }
 357
 358                 out << endl;
 359
 360                 int totalChildrenInTree = 0;
 361
 362                 map<string,int>::iterator it;
 363                 for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
 364                         if (tree[it->second].total != 0)  {   totalChildrenInTree++; }
 365                 }
 366
 367                 //print root
 368                 out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
 369
 370                 map<string, int>::iterator itGroup;
 371                 if (groupmap != NULL) {
 372                         //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
 373                         //      out << itGroup->second << '\t';
 374                         //}
 375                         for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[0].groupCount[groupmap->namesOfGroups[i]] << '\t'; }
 376                 }
 377                 out << endl;
 378
 379                 //print rest
 380                 print(0, out);
 381
 382         }
 383         catch(exception& e) {
 384                 m->errorOut(e, "PhyloSummary", "print");
 385                 exit(1);
 386         }
 387 }
 388
 389 /**************************************************************************************************/
 390
 391 void PhyloSummary::print(int i, ofstream& out){
 392         try {
 393                 map<string,int>::iterator it;
 394                 for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
 395
 396                         if (tree[it->second].total != 0)  {
 397
 398                                 int totalChildrenInTree = 0;
 399
 400                                 map<string,int>::iterator it2;
 401                                 for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
 402                                         if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
 403                                 }
 404
 405                                 out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
 406
 407                                 map<string, int>::iterator itGroup;
 408                                 if (groupmap != NULL) {
 409                                         //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
 410                                         //      out << itGroup->second << '\t';
 411                                         //}
 412                                         for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[it->second].groupCount[groupmap->namesOfGroups[i]] << '\t'; }
 413                                 }
 414                                 out << endl;
 415
 416                         }
 417
 418                         print(it->second, out);
 419                 }
 420         }
 421         catch(exception& e) {
 422                 m->errorOut(e, "PhyloSummary", "print");
 423                 exit(1);
 424         }
 425 }
 426 /**************************************************************************************************/
 427 void PhyloSummary::readTreeStruct(ifstream& in){
 428         try {
 429
 430                 //read version
 431                 string line = m->getline(in); m->gobble(in);
 432
 433                 int num;
 434
 435                 in >> num; m->gobble(in);
 436
 437                 tree.resize(num);
 438
 439                 in >> maxLevel; m->gobble(in);
 440
 441                 //read the tree file
 442                 for (int i = 0; i < tree.size(); i++) {
 443
 444                         in >> tree[i].level >> tree[i].name >> num; //num contains the number of children tree[i] has
 445
 446                         //set children
 447                         string childName;
 448                         int childIndex;
 449                         for (int j = 0; j < num; j++) {
 450                                 in >> childName >> childIndex;
 451                                 tree[i].children[childName] = childIndex;
 452                         }
 453
 454                         //initialize groupcounts
 455                         if (groupmap != NULL) {
 456                                 for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
 457                                         tree[i].groupCount[groupmap->namesOfGroups[j]] = 0;
 458                                 }
 459                         }
 460
 461                         tree[i].total = 0;
 462
 463                         m->gobble(in);
 464
 465                         //if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
 466                 }
 467
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "PhyloSummary", "print");
 471                 exit(1);
 472         }
 473 }
 474
 475 /**************************************************************************************************/
 476
 477
 478