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                     vector<string> names;
  89                     m->splitAtChar(second, names, ',');
  90
  91                     //get aligned string for these seqs from the fasta file
  92                     string alignedString = "";
  93                     map<string, string>::iterator itAligned = seqName.find(names[0]);
  94                     if (itAligned == seqName.end()) {
  95                         error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
  96                     }else {
  97                         alignedString = itAligned->second;
  98                     }
  99
 100                     //separate by group - parse one line in name file
 101                     map<string, string> splitMap; //group -> name1,name2,...
 102                     map<string, string>::iterator it;
 103                     for (int i = 0; i < names.size(); i++) {
 104
 105                         string group = groupMap->getGroup(names[i]);
 106                         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();  }
 107                         else {
 108
 109                             it = splitMap.find(group);
 110                             if (it != splitMap.end()) { //adding seqs to this group
 111                                 (it->second) += "," + names[i];
 112                                 thisnames1.insert(names[i]);
 113                                 countName++;
 114                             }else { //first sighting of this group
 115                                 splitMap[group] = names[i];
 116                                 countName++;
 117                                 thisnames1.insert(names[i]);
 118
 119                                 //is this seq in the fasta file?
 120                                 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
 121                                     Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
 122                                     seqs[group].push_back(tempSeq);
 123                                 }
 124                             }
 125                         }
 126
 127                         allSeqsMap[names[i]] = names[0];
 128                     }
 129
 130
 131                     //fill nameMapPerGroup - holds all lines in namefile separated by group
 132                     for (it = splitMap.begin(); it != splitMap.end(); it++) {
 133                         //grab first name
 134                         string firstName = "";
 135                         for(int i = 0; i < (it->second).length(); i++) {
 136                             if (((it->second)[i]) != ',') {
 137                                 firstName += ((it->second)[i]);
 138                             }else { break; }
 139                         }
 140
 141                         //group1 -> seq1 -> seq1,seq2,seq3
 142                         nameMapPerGroup[it->first][firstName] = it->second;
 143                     }
 144
 145                     pairDone = false;
 146                 }
 147             }
 148                 }
 149                 inName.close();
 150
 151                 if (error == 1) { m->control_pressed = true; }
 152
 153                 if (countName != (groupMap->getNumSeqs())) {
 154                         vector<string> groupseqsnames = groupMap->getNamesSeqs();
 155
 156                         for (int i = 0; i < groupseqsnames.size(); i++) {
 157                                 set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
 158                                 if (itnamesfile == thisnames1.end()){
 159                                         cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
 160                                 }
 161                         }
 162
 163                         m->mothurOutEndLine();
 164                         m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 165                         m->mothurOutEndLine();
 166                         m->control_pressed = true;
 167                 }
 168
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "SequenceParser", "SequenceParser");
 172                 exit(1);
 173         }
 174 }
 175 /************************************************************/
 176 SequenceParser::SequenceParser(string groupFile, string fastaFile) {
 177         try {
 178
 179                 m = MothurOut::getInstance();
 180                 int error;
 181
 182                 //read group file
 183                 groupMap = new GroupMap(groupFile);
 184                 error = groupMap->readMap();
 185
 186                 if (error == 1) { m->control_pressed = true; }
 187
 188                 //initialize maps
 189                 vector<string> namesOfGroups = groupMap->getNamesOfGroups();
 190                 for (int i = 0; i < namesOfGroups.size(); i++) {
 191                         vector<Sequence> temp;
 192                         seqs[namesOfGroups[i]] = temp;
 193                 }
 194
 195                 //read fasta file making sure each sequence is in the group file
 196                 ifstream in;
 197                 m->openInputFile(fastaFile, in);
 198                 int count = 0;
 199
 200                 while (!in.eof()) {
 201
 202                         if (m->control_pressed) { break; }
 203
 204                         Sequence seq(in); m->gobble(in);
 205
 206                         if (seq.getName() != "") {
 207
 208                                 string group = groupMap->getGroup(seq.getName());
 209                                 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();  }
 210                                 else {  seqs[group].push_back(seq);     count++; }
 211                         }
 212                 }
 213                 in.close();
 214
 215                 if (error == 1) { m->control_pressed = true; }
 216
 217                 if (count != (groupMap->getNumSeqs())) {
 218                         m->mothurOutEndLine();
 219                         m->mothurOut("[ERROR]: Your fasta file contains " + toString(count) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 220                         if (count < (groupMap->getNumSeqs())) { m->mothurOut(" Did you forget to include the name file?"); }
 221                         m->mothurOutEndLine();
 222                         m->control_pressed = true;
 223                 }
 224
 225         }
 226         catch(exception& e) {
 227                 m->errorOut(e, "SequenceParser", "SequenceParser");
 228                 exit(1);
 229         }
 230 }
 231 /************************************************************/
 232 SequenceParser::~SequenceParser(){ delete groupMap; }
 233 /************************************************************/
 234 int SequenceParser::getNumGroups(){ return groupMap->getNumGroups(); }
 235 /************************************************************/
 236 vector<string> SequenceParser::getNamesOfGroups(){ return groupMap->getNamesOfGroups(); }
 237 /************************************************************/
 238 bool SequenceParser::isValidGroup(string g){ return groupMap->isValidGroup(g); }
 239 /************************************************************/
 240 string SequenceParser::getGroup(string g){ return groupMap->getGroup(g); }
 241 /************************************************************/
 242 int SequenceParser::getNumSeqs(string g){
 243         try {
 244                 map<string, vector<Sequence> >::iterator it;
 245                 int num = 0;
 246
 247                 it = seqs.find(g);
 248                 if(it == seqs.end()) {
 249                         m->mothurOut("[ERROR]: " + g + " is not a valid group, please correct."); m->mothurOutEndLine();
 250                 }else {
 251                         num = (it->second).size();
 252                 }
 253
 254                 return num;
 255         }
 256         catch(exception& e) {
 257                 m->errorOut(e, "SequenceParser", "getNumSeqs");
 258                 exit(1);
 259         }
 260 }
 261 /************************************************************/
 262 vector<Sequence> SequenceParser::getSeqs(string g){
 263         try {
 264                 map<string, vector<Sequence> >::iterator it;
 265                 vector<Sequence> seqForThisGroup;
 266
 267                 it = seqs.find(g);
 268                 if(it == seqs.end()) {
 269                         m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 270                 }else {
 271                         seqForThisGroup = it->second;
 272             if (m->debug) {  m->mothurOut("[DEBUG]: group " + g + " fasta file has " + toString(seqForThisGroup.size()) + " sequences.");  }
 273                 }
 274
 275                 return seqForThisGroup;
 276         }
 277         catch(exception& e) {
 278                 m->errorOut(e, "SequenceParser", "getSeqs");
 279                 exit(1);
 280         }
 281 }
 282 /************************************************************/
 283 int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
 284         try {
 285                 map<string, vector<Sequence> >::iterator it;
 286                 vector<Sequence> seqForThisGroup;
 287                 vector<seqPriorityNode> nameVector;
 288
 289                 it = seqs.find(g);
 290                 if(it == seqs.end()) {
 291                         m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 292                 }else {
 293
 294                         ofstream out;
 295                         m->openOutputFile(filename, out);
 296
 297                         seqForThisGroup = it->second;
 298
 299                         if (uchimeFormat) {
 300                                 // format should look like
 301                                 //>seqName /ab=numRedundantSeqs/
 302                                 //sequence
 303
 304                                 map<string, string> nameMapForThisGroup = getNameMap(g);
 305                                 map<string, string>::iterator itNameMap;
 306                                 int error = 0;
 307
 308                                 for (int i = 0; i < seqForThisGroup.size(); i++) {
 309                                         itNameMap = nameMapForThisGroup.find(seqForThisGroup[i].getName());
 310
 311                                         if (itNameMap == nameMapForThisGroup.end()){
 312                                                 error = 1;
 313                                                 m->mothurOut("[ERROR]: " + seqForThisGroup[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
 314                                         }else {
 315                                                 int num = m->getNumNames(itNameMap->second);
 316
 317                                                 seqPriorityNode temp(num, seqForThisGroup[i].getAligned(), seqForThisGroup[i].getName());
 318                                                 nameVector.push_back(temp);
 319                                         }
 320                                 }
 321
 322                                 if (error == 1) { out.close(); m->mothurRemove(filename); return 1; }
 323
 324                                 //sort by num represented
 325                                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
 326
 327                                 //print new file in order of
 328                                 for (int i = 0; i < nameVector.size(); i++) {
 329
 330                                         if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 331
 332                                         out << ">" << nameVector[i].name  << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
 333                                 }
 334
 335                         }else {
 336                 //m->mothurOut("Group " + g +  " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
 337                                 for (int i = 0; i < seqForThisGroup.size(); i++) {
 338
 339                                         if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 340
 341                                         seqForThisGroup[i].printSequence(out);
 342                                 }
 343                         }
 344                         out.close();
 345                 }
 346
 347                 return 0;
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "SequenceParser", "getSeqs");
 351                 exit(1);
 352         }
 353 }
 354
 355 /************************************************************/
 356 map<string, string> SequenceParser::getNameMap(string g){
 357         try {
 358                 map<string, map<string, string> >::iterator it;
 359                 map<string, string> nameMapForThisGroup;
 360
 361                 it = nameMapPerGroup.find(g);
 362                 if(it == nameMapPerGroup.end()) {
 363                         m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
 364                 }else {
 365                         nameMapForThisGroup = it->second;
 366             if (m->debug) {  m->mothurOut("[DEBUG]: group " + g + " name file has " + toString(nameMapForThisGroup.size()) + " unique sequences.");  }
 367                 }
 368
 369                 return nameMapForThisGroup;
 370         }
 371         catch(exception& e) {
 372                 m->errorOut(e, "SequenceParser", "getNameMap");
 373                 exit(1);
 374         }
 375 }
 376 /************************************************************/
 377 int SequenceParser::getNameMap(string g, string filename){
 378         try {
 379                 map<string, map<string, string> >::iterator it;
 380                 map<string, string> nameMapForThisGroup;
 381
 382                 it = nameMapPerGroup.find(g);
 383                 if(it == nameMapPerGroup.end()) {
 384                         m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
 385                 }else {
 386                         nameMapForThisGroup = it->second;
 387
 388                         ofstream out;
 389                         m->openOutputFile(filename, out);
 390
 391                         for (map<string, string>::iterator itFile = nameMapForThisGroup.begin(); itFile != nameMapForThisGroup.end(); itFile++) {
 392
 393                                 if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 394
 395                                 out << itFile->first << '\t' << itFile->second << endl;
 396                         }
 397
 398                         out.close();
 399                 }
 400
 401                 return 0;
 402         }
 403         catch(exception& e) {
 404                 m->errorOut(e, "SequenceParser", "getNameMap");
 405                 exit(1);
 406         }
 407 }
 408 /************************************************************/
 409
 410
 411