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                                                 vector<string> mGroups = groupmap->getNamesOfGroups();
 172                                                 for (int j = 0; j < mGroups.size(); j++) {
 173                                                         tree[index].groupCount[mGroups[j]] = 0;
 174                                                 }
 175
 176                                                 //find out the sequences group
 177                                                 string group = groupmap->getGroup(seqName);
 178
 179                                                 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();  }
 180
 181                                                 //do you have a count for this group?
 182                                                 map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
 183
 184                                                 //if yes, increment it - there should not be a case where we can't find it since we load group in read
 185                                                 if (itGroup != tree[index].groupCount.end()) {
 186                                                         tree[index].groupCount[group]++;
 187                                                 }
 188                                         }
 189
 190                                         currentNode = index;
 191
 192                                 }else{ //otherwise, error
 193                                         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();
 194                                         break;
 195                                 }
 196                         }
 197
 198                         level++;
 199
 200                         if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
 201                                 for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
 202                         }
 203                 }
 204                 return 0;
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "PhyloSummary", "addSeqToTree");
 208                 exit(1);
 209         }
 210 }
 211 /**************************************************************************************************/
 212
 213 int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 214         try {
 215                 numSeqs++;
 216
 217                 map<string, int>::iterator childPointer;
 218
 219                 int currentNode = 0;
 220                 string taxon;
 221
 222                 int level = 0;
 223
 224                 while (seqTaxonomy != "") {
 225
 226                         if (m->control_pressed) { return 0; }
 227
 228                         //somehow the parent is getting one too many accnos
 229                         //use print to reassign the taxa id
 230                         taxon = getNextTaxon(seqTaxonomy);
 231
 232                         childPointer = tree[currentNode].children.find(taxon);
 233
 234                         if(childPointer != tree[currentNode].children.end()){   //if the node already exists, update count and move on
 235                                 if (groupmap != NULL) {
 236
 237                                         map<string, bool> containsGroup;
 238                                         vector<string> mGroups = groupmap->getNamesOfGroups();
 239                                         for (int j = 0; j < mGroups.size(); j++) {
 240                                                 containsGroup[mGroups[j]] = false;
 241                                         }
 242
 243                                         for (int k = 0; k < names.size(); k++) {
 244                                                 //find out the sequences group
 245                                                 string group = groupmap->getGroup(names[k]);
 246
 247                                                 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();  }
 248                                                 else {
 249                                                         containsGroup[group] = true;
 250                                                 }
 251                                         }
 252
 253                                         for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
 254                                                 if (itGroup->second == true) {
 255                                                         tree[childPointer->second].groupCount[itGroup->first]++;
 256                                                 }
 257                                         }
 258
 259                                 }
 260
 261                                 tree[childPointer->second].total++;
 262
 263                                 currentNode = childPointer->second;
 264                         }else{
 265                                 if (ignore) {
 266
 267                                         tree.push_back(rawTaxNode(taxon));
 268                                         int index = tree.size() - 1;
 269
 270                                         tree[index].parent = currentNode;
 271                                         tree[index].level = (level+1);
 272                                         tree[index].total = 1;
 273                                         tree[currentNode].children[taxon] = index;
 274
 275                                         //initialize groupcounts
 276                                         if (groupmap != NULL) {
 277                                                 map<string, bool> containsGroup;
 278                                                 vector<string> mGroups = groupmap->getNamesOfGroups();
 279                                                 for (int j = 0; j < mGroups.size(); j++) {
 280                                                         tree[index].groupCount[mGroups[j]] = 0;
 281                                                         containsGroup[mGroups[j]] = false;
 282                                                 }
 283
 284
 285                                                 for (int k = 0; k < names.size(); k++) {
 286                                                         //find out the sequences group
 287                                                         string group = groupmap->getGroup(names[k]);
 288
 289                                                         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();  }
 290                                                         else {
 291                                                                 containsGroup[group] = true;
 292                                                         }
 293                                                 }
 294
 295                                                 for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
 296                                                         if (itGroup->second == true) {
 297                                                                 tree[index].groupCount[itGroup->first]++;
 298                                                         }
 299                                                 }
 300                                         }
 301
 302                                         currentNode = index;
 303
 304                                 }else{ //otherwise, error
 305                                         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();
 306                                         break;
 307                                 }
 308                         }
 309
 310                         level++;
 311
 312                         if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
 313                                 for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
 314                         }
 315                 }
 316                 return 0;
 317         }
 318         catch(exception& e) {
 319                 m->errorOut(e, "PhyloSummary", "addSeqToTree");
 320                 exit(1);
 321         }
 322 }
 323
 324 /**************************************************************************************************/
 325
 326 void PhyloSummary::assignRank(int index){
 327         try {
 328                 map<string,int>::iterator it;
 329                 int counter = 1;
 330
 331                 for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
 332                         tree[it->second].rank = tree[index].rank + '.' + toString(counter);
 333                         counter++;
 334
 335                         assignRank(it->second);
 336                 }
 337         }
 338         catch(exception& e) {
 339                 m->errorOut(e, "PhyloSummary", "assignRank");
 340                 exit(1);
 341         }
 342 }
 343 /**************************************************************************************************/
 344
 345 void PhyloSummary::print(ofstream& out){
 346         try {
 347
 348                 if (ignore) { assignRank(0); }
 349
 350                 //print labels
 351                 out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
 352                 if (groupmap != NULL) {
 353                         //so the labels match the counts below, since the map sorts them automatically...
 354                         //sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
 355                         vector<string> mGroups = groupmap->getNamesOfGroups();
 356                         for (int i = 0; i < mGroups.size(); i++) {
 357                                 out << mGroups[i] << '\t';
 358                         }
 359                 }
 360
 361                 out << endl;
 362
 363                 int totalChildrenInTree = 0;
 364
 365                 map<string,int>::iterator it;
 366                 for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
 367                         if (tree[it->second].total != 0)  {   totalChildrenInTree++; }
 368                 }
 369
 370                 //print root
 371                 out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
 372
 373                 map<string, int>::iterator itGroup;
 374                 if (groupmap != NULL) {
 375                         //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
 376                         //      out << itGroup->second << '\t';
 377                         //}
 378                         vector<string> mGroups = groupmap->getNamesOfGroups();
 379                         for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; }
 380                 }
 381                 out << endl;
 382
 383                 //print rest
 384                 print(0, out);
 385
 386         }
 387         catch(exception& e) {
 388                 m->errorOut(e, "PhyloSummary", "print");
 389                 exit(1);
 390         }
 391 }
 392
 393 /**************************************************************************************************/
 394
 395 void PhyloSummary::print(int i, ofstream& out){
 396         try {
 397                 map<string,int>::iterator it;
 398                 for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
 399
 400                         if (tree[it->second].total != 0)  {
 401
 402                                 int totalChildrenInTree = 0;
 403
 404                                 map<string,int>::iterator it2;
 405                                 for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
 406                                         if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
 407                                 }
 408
 409                                 out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
 410
 411                                 map<string, int>::iterator itGroup;
 412                                 if (groupmap != NULL) {
 413                                         //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
 414                                         //      out << itGroup->second << '\t';
 415                                         //}
 416                                         vector<string> mGroups = groupmap->getNamesOfGroups();
 417                                         for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
 418                                 }
 419                                 out << endl;
 420
 421                         }
 422
 423                         print(it->second, out);
 424                 }
 425         }
 426         catch(exception& e) {
 427                 m->errorOut(e, "PhyloSummary", "print");
 428                 exit(1);
 429         }
 430 }
 431 /**************************************************************************************************/
 432 void PhyloSummary::readTreeStruct(ifstream& in){
 433         try {
 434
 435                 //read version
 436                 string line = m->getline(in); m->gobble(in);
 437
 438                 int num;
 439
 440                 in >> num; m->gobble(in);
 441
 442                 tree.resize(num);
 443
 444                 in >> maxLevel; m->gobble(in);
 445
 446                 //read the tree file
 447                 for (int i = 0; i < tree.size(); i++) {
 448
 449                         in >> tree[i].level >> tree[i].name >> num; //num contains the number of children tree[i] has
 450
 451                         //set children
 452                         string childName;
 453                         int childIndex;
 454                         for (int j = 0; j < num; j++) {
 455                                 in >> childName >> childIndex;
 456                                 tree[i].children[childName] = childIndex;
 457                         }
 458
 459                         //initialize groupcounts
 460                         if (groupmap != NULL) {
 461                                 for (int j = 0; j < (groupmap->getNamesOfGroups()).size(); j++) {
 462                                         tree[i].groupCount[(groupmap->getNamesOfGroups())[j]] = 0;
 463                                 }
 464                         }
 465
 466                         tree[i].total = 0;
 467
 468                         m->gobble(in);
 469
 470                         //if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
 471                 }
 472
 473         }
 474         catch(exception& e) {
 475                 m->errorOut(e, "PhyloSummary", "print");
 476                 exit(1);
 477         }
 478 }
 479
 480 /**************************************************************************************************/
 481
 482
 483