sequenceparser.cpp

   1 /*
   2  *  sequenceParser.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/9/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sequenceparser.h"
  11
  12
  13 /************************************************************/
  14 SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFile) {
  15         try {
  16
  17                 m = MothurOut::getInstance();
  18                 int error;
  19
  20                 //read group file
  21                 groupMap = new GroupMap(groupFile);
  22                 error = groupMap->readMap();
  23
  24                 if (error == 1) { m->control_pressed = true; }
  25
  26                 //initialize maps
  27                 vector<string> namesOfGroups = groupMap->getNamesOfGroups();
  28                 for (int i = 0; i < namesOfGroups.size(); i++) {
  29                         vector<Sequence> temp;
  30                         map<string, string> tempMap;
  31                         seqs[namesOfGroups[i]] = temp;
  32                         nameMapPerGroup[namesOfGroups[i]] = tempMap;
  33                 }
  34
  35                 //read fasta file making sure each sequence is in the group file
  36                 ifstream in;
  37                 m->openInputFile(fastaFile, in);
  38
  39                 map<string, string> seqName; //stores name -> sequence string so we can make new "unique" sequences when we parse the name file
  40         int fastaCount = 0;
  41                 while (!in.eof()) {
  42
  43                         if (m->control_pressed) { break; }
  44
  45                         Sequence seq(in); m->gobble(in);
  46             fastaCount++;
  47             if (m->debug) { if((fastaCount) % 1000 == 0){       m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n.");   } }
  48
  49         if (seq.getName() != "") {
  50
  51                                  string group = groupMap->getGroup(seq.getName());
  52                                  if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
  53                                  else {
  54                                          seqs[group].push_back(seq);
  55                                          seqName[seq.getName()] = seq.getAligned();
  56                                  }
  57                         }
  58                 }
  59                 in.close();
  60
  61                 if (error == 1) { m->control_pressed = true; }
  62
  63                 //read name file
  64                 ifstream inName;
  65                 m->openInputFile(nameFile, inName);
  66
  67                 //string first, second;
  68                 int countName = 0;
  69                 set<string> thisnames1;
  70
  71         string rest = "";
  72         char buffer[4096];
  73         bool pairDone = false;
  74         bool columnOne = true;
  75         string firstCol, secondCol;
  76
  77                 while (!inName.eof()) {
  78                         if (m->control_pressed) { break; }
  79
  80             inName.read(buffer, 4096);
  81             vector<string> pieces = m->splitWhiteSpace(rest, buffer, inName.gcount());
  82
  83             for (int i = 0; i < pieces.size(); i++) {
  84                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
  85                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
  86
  87                 if (pairDone) { //save one line
  88                     if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
  89                     vector<string> names;
  90                     m->splitAtChar(secondCol, names, ',');
  91
  92                     //get aligned string for these seqs from the fasta file
  93                     string alignedString = "";
  94                     map<string, string>::iterator itAligned = seqName.find(names[0]);
  95                     if (itAligned == seqName.end()) {
  96                         error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
  97                     }else {
  98                         alignedString = itAligned->second;
  99                     }
 100
 101                     //separate by group - parse one line in name file
 102                     map<string, string> splitMap; //group -> name1,name2,...
 103                     map<string, string>::iterator it;
 104                     for (int i = 0; i < names.size(); i++) {
 105
 106                         string group = groupMap->getGroup(names[i]);
 107                         if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
 108                         else {
 109
 110                             it = splitMap.find(group);
 111                             if (it != splitMap.end()) { //adding seqs to this group
 112                                 (it->second) += "," + names[i];
 113                                 thisnames1.insert(names[i]);
 114                                 countName++;
 115                             }else { //first sighting of this group
 116                                 splitMap[group] = names[i];
 117                                 countName++;
 118                                 thisnames1.insert(names[i]);
 119
 120                                 //is this seq in the fasta file?
 121                                 if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
 122                                     Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
 123                                     seqs[group].push_back(tempSeq);
 124                                 }
 125                             }
 126                         }
 127
 128                         allSeqsMap[names[i]] = names[0];
 129                     }
 130
 131
 132                     //fill nameMapPerGroup - holds all lines in namefile separated by group
 133                     for (it = splitMap.begin(); it != splitMap.end(); it++) {
 134                         //grab first name
 135                         string firstName = "";
 136                         for(int i = 0; i < (it->second).length(); i++) {
 137                             if (((it->second)[i]) != ',') {
 138                                 firstName += ((it->second)[i]);
 139                             }else { break; }
 140                         }
 141
 142                         //group1 -> seq1 -> seq1,seq2,seq3
 143                         nameMapPerGroup[it->first][firstName] = it->second;
 144                     }
 145
 146                     pairDone = false;
 147                 }
 148             }
 149                 }
 150                 inName.close();
 151
 152         //in case file does not end in white space
 153         if (rest != "") {
 154             vector<string> pieces = m->splitWhiteSpace(rest);
 155
 156             for (int i = 0; i < pieces.size(); i++) {
 157                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 158                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 159
 160                 if (pairDone) { //save one line
 161                     if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
 162                     vector<string> names;
 163                     m->splitAtChar(secondCol, names, ',');
 164
 165                     //get aligned string for these seqs from the fasta file
 166                     string alignedString = "";
 167                     map<string, string>::iterator itAligned = seqName.find(names[0]);
 168                     if (itAligned == seqName.end()) {
 169                         error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
 170                     }else {
 171                         alignedString = itAligned->second;
 172                     }
 173
 174                     //separate by group - parse one line in name file
 175                     map<string, string> splitMap; //group -> name1,name2,...
 176                     map<string, string>::iterator it;
 177                     for (int i = 0; i < names.size(); i++) {
 178
 179                         string group = groupMap->getGroup(names[i]);
 180                         if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
 181                         else {
 182
 183                             it = splitMap.find(group);
 184                             if (it != splitMap.end()) { //adding seqs to this group
 185                                 (it->second) += "," + names[i];
 186                                 thisnames1.insert(names[i]);
 187                                 countName++;
 188                             }else { //first sighting of this group
 189                                 splitMap[group] = names[i];
 190                                 countName++;
 191                                 thisnames1.insert(names[i]);
 192
 193                                 //is this seq in the fasta file?
 194                                 if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
 195                                     Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
 196                                     seqs[group].push_back(tempSeq);
 197                                 }
 198                             }
 199                         }
 200
 201                         allSeqsMap[names[i]] = names[0];
 202                     }
 203
 204
 205                     //fill nameMapPerGroup - holds all lines in namefile separated by group
 206                     for (it = splitMap.begin(); it != splitMap.end(); it++) {
 207                         //grab first name
 208                         string firstName = "";
 209                         for(int i = 0; i < (it->second).length(); i++) {
 210                             if (((it->second)[i]) != ',') {
 211                                 firstName += ((it->second)[i]);
 212                             }else { break; }
 213                         }
 214
 215                         //group1 -> seq1 -> seq1,seq2,seq3
 216                         nameMapPerGroup[it->first][firstName] = it->second;
 217                     }
 218
 219                     pairDone = false;
 220                 }
 221             }
 222         }
 223
 224                 if (error == 1) { m->control_pressed = true; }
 225
 226                 if (countName != (groupMap->getNumSeqs())) {
 227                         vector<string> groupseqsnames = groupMap->getNamesSeqs();
 228
 229                         for (int i = 0; i < groupseqsnames.size(); i++) {
 230                                 set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
 231                                 if (itnamesfile == thisnames1.end()){
 232                                         cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
 233                                 }
 234                         }
 235
 236                         m->mothurOutEndLine();
 237                         m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 238                         m->mothurOutEndLine();
 239                         m->control_pressed = true;
 240                 }
 241
 242         }
 243         catch(exception& e) {
 244                 m->errorOut(e, "SequenceParser", "SequenceParser");
 245                 exit(1);
 246         }
 247 }
 248 /************************************************************/
 249 SequenceParser::SequenceParser(string groupFile, string fastaFile) {
 250         try {
 251
 252                 m = MothurOut::getInstance();
 253                 int error;
 254
 255                 //read group file
 256                 groupMap = new GroupMap(groupFile);
 257                 error = groupMap->readMap();
 258
 259                 if (error == 1) { m->control_pressed = true; }
 260
 261                 //initialize maps
 262                 vector<string> namesOfGroups = groupMap->getNamesOfGroups();
 263                 for (int i = 0; i < namesOfGroups.size(); i++) {
 264                         vector<Sequence> temp;
 265                         seqs[namesOfGroups[i]] = temp;
 266                 }
 267
 268                 //read fasta file making sure each sequence is in the group file
 269                 ifstream in;
 270                 m->openInputFile(fastaFile, in);
 271                 int count = 0;
 272
 273                 while (!in.eof()) {
 274
 275                         if (m->control_pressed) { break; }
 276
 277                         Sequence seq(in); m->gobble(in);
 278
 279                         if (seq.getName() != "") {
 280
 281                                 string group = groupMap->getGroup(seq.getName());
 282                                 if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
 283                                 else {  seqs[group].push_back(seq);     count++; }
 284                         }
 285                 }
 286                 in.close();
 287
 288                 if (error == 1) { m->control_pressed = true; }
 289
 290                 if (count != (groupMap->getNumSeqs())) {
 291                         m->mothurOutEndLine();
 292                         m->mothurOut("[ERROR]: Your fasta file contains " + toString(count) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 293                         if (count < (groupMap->getNumSeqs())) { m->mothurOut(" Did you forget to include the name file?"); }
 294                         m->mothurOutEndLine();
 295                         m->control_pressed = true;
 296                 }
 297
 298         }
 299         catch(exception& e) {
 300                 m->errorOut(e, "SequenceParser", "SequenceParser");
 301                 exit(1);
 302         }
 303 }
 304 /************************************************************/
 305 SequenceParser::~SequenceParser(){ delete groupMap; }
 306 /************************************************************/
 307 int SequenceParser::getNumGroups(){ return groupMap->getNumGroups(); }
 308 /************************************************************/
 309 vector<string> SequenceParser::getNamesOfGroups(){ return groupMap->getNamesOfGroups(); }
 310 /************************************************************/
 311 bool SequenceParser::isValidGroup(string g){ return groupMap->isValidGroup(g); }
 312 /************************************************************/
 313 int SequenceParser::getNumSeqs(string g){
 314         try {
 315                 map<string, vector<Sequence> >::iterator it;
 316                 int num = 0;
 317
 318                 it = seqs.find(g);
 319                 if(it == seqs.end()) {
 320                         m->mothurOut("[ERROR]: " + g + " is not a valid group, please correct."); m->mothurOutEndLine();
 321                 }else {
 322                         num = (it->second).size();
 323                 }
 324
 325                 return num;
 326         }
 327         catch(exception& e) {
 328                 m->errorOut(e, "SequenceParser", "getNumSeqs");
 329                 exit(1);
 330         }
 331 }
 332 /************************************************************/
 333 vector<Sequence> SequenceParser::getSeqs(string g){
 334         try {
 335                 map<string, vector<Sequence> >::iterator it;
 336                 vector<Sequence> seqForThisGroup;
 337
 338                 it = seqs.find(g);
 339                 if(it == seqs.end()) {
 340                         m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 341                 }else {
 342                         seqForThisGroup = it->second;
 343             if (m->debug) {  m->mothurOut("[DEBUG]: group " + g + " fasta file has " + toString(seqForThisGroup.size()) + " sequences.");  }
 344                 }
 345
 346                 return seqForThisGroup;
 347         }
 348         catch(exception& e) {
 349                 m->errorOut(e, "SequenceParser", "getSeqs");
 350                 exit(1);
 351         }
 352 }
 353 /************************************************************/
 354 int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
 355         try {
 356                 map<string, vector<Sequence> >::iterator it;
 357                 vector<Sequence> seqForThisGroup;
 358                 vector<seqPriorityNode> nameVector;
 359
 360                 it = seqs.find(g);
 361                 if(it == seqs.end()) {
 362                         m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 363                 }else {
 364
 365                         ofstream out;
 366                         m->openOutputFile(filename, out);
 367
 368                         seqForThisGroup = it->second;
 369
 370                         if (uchimeFormat) {
 371                                 // format should look like
 372                                 //>seqName /ab=numRedundantSeqs/
 373                                 //sequence
 374
 375                                 map<string, string> nameMapForThisGroup = getNameMap(g);
 376                                 map<string, string>::iterator itNameMap;
 377                                 int error = 0;
 378
 379                                 for (int i = 0; i < seqForThisGroup.size(); i++) {
 380                                         itNameMap = nameMapForThisGroup.find(seqForThisGroup[i].getName());
 381
 382                                         if (itNameMap == nameMapForThisGroup.end()){
 383                                                 error = 1;
 384                                                 m->mothurOut("[ERROR]: " + seqForThisGroup[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
 385                                         }else {
 386                                                 int num = m->getNumNames(itNameMap->second);
 387
 388                                                 seqPriorityNode temp(num, seqForThisGroup[i].getAligned(), seqForThisGroup[i].getName());
 389                                                 nameVector.push_back(temp);
 390                                         }
 391                                 }
 392
 393                                 if (error == 1) { out.close(); m->mothurRemove(filename); return 1; }
 394
 395                                 //sort by num represented
 396                                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
 397
 398                                 //print new file in order of
 399                                 for (int i = 0; i < nameVector.size(); i++) {
 400
 401                                         if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 402
 403                                         out << ">" <<  nameVector[i].name << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl; //
 404                                 }
 405
 406                         }else {
 407                 //m->mothurOut("Group " + g +  " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
 408                                 for (int i = 0; i < seqForThisGroup.size(); i++) {
 409
 410                                         if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 411
 412                                         seqForThisGroup[i].printSequence(out);
 413                                 }
 414                         }
 415                         out.close();
 416                 }
 417
 418                 return 0;
 419         }
 420         catch(exception& e) {
 421                 m->errorOut(e, "SequenceParser", "getSeqs");
 422                 exit(1);
 423         }
 424 }
 425
 426 /************************************************************/
 427 map<string, string> SequenceParser::getNameMap(string g){
 428         try {
 429                 map<string, map<string, string> >::iterator it;
 430                 map<string, string> nameMapForThisGroup;
 431
 432                 it = nameMapPerGroup.find(g);
 433                 if(it == nameMapPerGroup.end()) {
 434                         m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
 435                 }else {
 436                         nameMapForThisGroup = it->second;
 437             if (m->debug) {  m->mothurOut("[DEBUG]: group " + g + " name file has " + toString(nameMapForThisGroup.size()) + " unique sequences.");  }
 438                 }
 439
 440                 return nameMapForThisGroup;
 441         }
 442         catch(exception& e) {
 443                 m->errorOut(e, "SequenceParser", "getNameMap");
 444                 exit(1);
 445         }
 446 }
 447 /************************************************************/
 448 int SequenceParser::getNameMap(string g, string filename){
 449         try {
 450                 map<string, map<string, string> >::iterator it;
 451                 map<string, string> nameMapForThisGroup;
 452
 453                 it = nameMapPerGroup.find(g);
 454                 if(it == nameMapPerGroup.end()) {
 455                         m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
 456                 }else {
 457                         nameMapForThisGroup = it->second;
 458
 459                         ofstream out;
 460                         m->openOutputFile(filename, out);
 461
 462                         for (map<string, string>::iterator itFile = nameMapForThisGroup.begin(); itFile != nameMapForThisGroup.end(); itFile++) {
 463
 464                                 if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 465
 466                                 out << itFile->first << '\t' << itFile->second << endl;
 467                         }
 468
 469                         out.close();
 470                 }
 471
 472                 return 0;
 473         }
 474         catch(exception& e) {
 475                 m->errorOut(e, "SequenceParser", "getNameMap");
 476                 exit(1);
 477         }
 478 }
 479 /************************************************************/
 480
 481
 482