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                 while (!in.eof()) {
  41
  42                         if (m->control_pressed) { break; }
  43
  44                         Sequence seq(in); m->gobble(in);
  45
  46                         if (seq.getName() != "") {
  47
  48                                  string group = groupMap->getGroup(seq.getName());
  49                                  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();  }
  50                                  else {
  51                                          seqs[group].push_back(seq);
  52                                          seqName[seq.getName()] = seq.getAligned();
  53                                  }
  54                         }
  55                 }
  56                 in.close();
  57
  58                 if (error == 1) { m->control_pressed = true; }
  59
  60                 //read name file
  61                 ifstream inName;
  62                 m->openInputFile(nameFile, inName);
  63
  64                 string first, second;
  65                 int countName = 0;
  66                 while(!inName.eof()) {
  67
  68                         if (m->control_pressed) { break; }
  69
  70                         inName >> first; m->gobble(inName);
  71                         inName >> second; m->gobble(inName);
  72
  73                         vector<string> names;
  74                         m->splitAtChar(second, names, ',');
  75
  76                         //get aligned string for these seqs from the fasta file
  77                         string alignedString = "";
  78                         map<string, string>::iterator itAligned = seqName.find(names[0]);
  79                         if (itAligned == seqName.end()) {
  80                                 error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
  81                         }else {
  82                                 alignedString = itAligned->second;
  83                         }
  84
  85                         //separate by group - parse one line in name file
  86                         map<string, string> splitMap; //group -> name1,name2,...
  87                         map<string, string>::iterator it;
  88                         for (int i = 0; i < names.size(); i++) {
  89
  90                                 string group = groupMap->getGroup(names[i]);
  91                                 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();  }
  92                                 else {
  93
  94                                         it = splitMap.find(group);
  95                                         if (it != splitMap.end()) { //adding seqs to this group
  96                                                 (it->second) += "," + names[i];
  97                                                 countName++;
  98                                         }else { //first sighting of this group
  99                                                 splitMap[group] = names[i];
 100                                                 countName++;
 101
 102                                                 //is this seq in the fasta file?
 103                                                 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
 104                                                         Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
 105                                                         seqs[group].push_back(tempSeq);
 106                                                 }
 107                                         }
 108                                 }
 109
 110                                 allSeqsMap[names[i]] = names[0];
 111                         }
 112
 113
 114                         //fill nameMapPerGroup - holds all lines in namefile separated by group
 115                         for (it = splitMap.begin(); it != splitMap.end(); it++) {
 116                                 //grab first name
 117                                 string firstName = "";
 118                                 for(int i = 0; i < (it->second).length(); i++) {
 119                                         if (((it->second)[i]) != ',') {
 120                                                 firstName += ((it->second)[i]);
 121                                         }else { break; }
 122                                 }
 123
 124                                 //group1 -> seq1 -> seq1,seq2,seq3
 125                                 nameMapPerGroup[it->first][firstName] = it->second;
 126                         }
 127                 }
 128
 129                 inName.close();
 130
 131                 if (error == 1) { m->control_pressed = true; }
 132
 133                 if (countName != (groupMap->getNumSeqs())) {
 134                         m->mothurOutEndLine();
 135                         m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 136                         m->mothurOutEndLine();
 137                         m->control_pressed = true;
 138                 }
 139
 140         }
 141         catch(exception& e) {
 142                 m->errorOut(e, "SequenceParser", "SequenceParser");
 143                 exit(1);
 144         }
 145 }
 146 /************************************************************/
 147 SequenceParser::SequenceParser(string groupFile, string fastaFile) {
 148         try {
 149
 150                 m = MothurOut::getInstance();
 151                 int error;
 152
 153                 //read group file
 154                 groupMap = new GroupMap(groupFile);
 155                 error = groupMap->readMap();
 156
 157                 if (error == 1) { m->control_pressed = true; }
 158
 159                 //initialize maps
 160                 vector<string> namesOfGroups = groupMap->getNamesOfGroups();
 161                 for (int i = 0; i < namesOfGroups.size(); i++) {
 162                         vector<Sequence> temp;
 163                         seqs[namesOfGroups[i]] = temp;
 164                 }
 165
 166                 //read fasta file making sure each sequence is in the group file
 167                 ifstream in;
 168                 m->openInputFile(fastaFile, in);
 169                 int count = 0;
 170
 171                 while (!in.eof()) {
 172
 173                         if (m->control_pressed) { break; }
 174
 175                         Sequence seq(in); m->gobble(in);
 176
 177                         if (seq.getName() != "") {
 178
 179                                 string group = groupMap->getGroup(seq.getName());
 180                                 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();  }
 181                                 else {  seqs[group].push_back(seq);     count++; }
 182                         }
 183                 }
 184                 in.close();
 185
 186                 if (error == 1) { m->control_pressed = true; }
 187
 188                 if (count != (groupMap->getNumSeqs())) {
 189                         m->mothurOutEndLine();
 190                         m->mothurOut("[ERROR]: Your fasta file contains " + toString(count) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 191                         if (count < (groupMap->getNumSeqs())) { m->mothurOut(" Did you forget to include the name file?"); }
 192                         m->mothurOutEndLine();
 193                         m->control_pressed = true;
 194                 }
 195
 196         }
 197         catch(exception& e) {
 198                 m->errorOut(e, "SequenceParser", "SequenceParser");
 199                 exit(1);
 200         }
 201 }
 202 /************************************************************/
 203 SequenceParser::~SequenceParser(){ delete groupMap; }
 204 /************************************************************/
 205 int SequenceParser::getNumGroups(){ return groupMap->getNumGroups(); }
 206 /************************************************************/
 207 vector<string> SequenceParser::getNamesOfGroups(){ return groupMap->getNamesOfGroups(); }
 208 /************************************************************/
 209 bool SequenceParser::isValidGroup(string g){ return groupMap->isValidGroup(g); }
 210 /************************************************************/
 211 string SequenceParser::getGroup(string g){ return groupMap->getGroup(g); }
 212 /************************************************************/
 213 int SequenceParser::getNumSeqs(string g){
 214         try {
 215                 map<string, vector<Sequence> >::iterator it;
 216                 int num = 0;
 217
 218                 it = seqs.find(g);
 219                 if(it == seqs.end()) {
 220                         m->mothurOut("[ERROR]: " + g + " is not a valid group, please correct."); m->mothurOutEndLine();
 221                 }else {
 222                         num = (it->second).size();
 223                 }
 224
 225                 return num;
 226         }
 227         catch(exception& e) {
 228                 m->errorOut(e, "SequenceParser", "getNumSeqs");
 229                 exit(1);
 230         }
 231 }
 232 /************************************************************/
 233 vector<Sequence> SequenceParser::getSeqs(string g){
 234         try {
 235                 map<string, vector<Sequence> >::iterator it;
 236                 vector<Sequence> seqForThisGroup;
 237
 238                 it = seqs.find(g);
 239                 if(it == seqs.end()) {
 240                         m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 241                 }else {
 242                         seqForThisGroup = it->second;
 243                 }
 244
 245                 return seqForThisGroup;
 246         }
 247         catch(exception& e) {
 248                 m->errorOut(e, "SequenceParser", "getSeqs");
 249                 exit(1);
 250         }
 251 }
 252 /************************************************************/
 253 int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
 254         try {
 255                 map<string, vector<Sequence> >::iterator it;
 256                 vector<Sequence> seqForThisGroup;
 257                 vector<seqPriorityNode> nameVector;
 258
 259                 it = seqs.find(g);
 260                 if(it == seqs.end()) {
 261                         m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 262                 }else {
 263
 264                         ofstream out;
 265                         m->openOutputFile(filename, out);
 266
 267                         seqForThisGroup = it->second;
 268
 269                         if (uchimeFormat) {
 270                                 // format should look like
 271                                 //>seqName /ab=numRedundantSeqs/
 272                                 //sequence
 273
 274                                 map<string, string> nameMapForThisGroup = getNameMap(g);
 275                                 map<string, string>::iterator itNameMap;
 276                                 int error = 0;
 277
 278                                 for (int i = 0; i < seqForThisGroup.size(); i++) {
 279                                         itNameMap = nameMapForThisGroup.find(seqForThisGroup[i].getName());
 280
 281                                         if (itNameMap == nameMapForThisGroup.end()){
 282                                                 error = 1;
 283                                                 m->mothurOut("[ERROR]: " + seqForThisGroup[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
 284                                         }else {
 285                                                 int num = m->getNumNames(itNameMap->second);
 286
 287                                                 seqPriorityNode temp(num, seqForThisGroup[i].getAligned(), seqForThisGroup[i].getName());
 288                                                 nameVector.push_back(temp);
 289                                         }
 290                                 }
 291
 292                                 if (error == 1) { out.close(); m->mothurRemove(filename); return 1; }
 293
 294                                 //sort by num represented
 295                                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
 296
 297                                 //print new file in order of
 298                                 for (int i = 0; i < nameVector.size(); i++) {
 299
 300                                         if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 301
 302                                         out << ">" << nameVector[i].name  << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
 303                                 }
 304
 305                         }else {
 306                                 for (int i = 0; i < seqForThisGroup.size(); i++) {
 307
 308                                         if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 309
 310                                         seqForThisGroup[i].printSequence(out);
 311                                 }
 312                         }
 313                         out.close();
 314                 }
 315
 316                 return 0;
 317         }
 318         catch(exception& e) {
 319                 m->errorOut(e, "SequenceParser", "getSeqs");
 320                 exit(1);
 321         }
 322 }
 323
 324 /************************************************************/
 325 map<string, string> SequenceParser::getNameMap(string g){
 326         try {
 327                 map<string, map<string, string> >::iterator it;
 328                 map<string, string> nameMapForThisGroup;
 329
 330                 it = nameMapPerGroup.find(g);
 331                 if(it == nameMapPerGroup.end()) {
 332                         m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
 333                 }else {
 334                         nameMapForThisGroup = it->second;
 335                 }
 336
 337                 return nameMapForThisGroup;
 338         }
 339         catch(exception& e) {
 340                 m->errorOut(e, "SequenceParser", "getNameMap");
 341                 exit(1);
 342         }
 343 }
 344 /************************************************************/
 345 int SequenceParser::getNameMap(string g, string filename){
 346         try {
 347                 map<string, map<string, string> >::iterator it;
 348                 map<string, string> nameMapForThisGroup;
 349
 350                 it = nameMapPerGroup.find(g);
 351                 if(it == nameMapPerGroup.end()) {
 352                         m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
 353                 }else {
 354                         nameMapForThisGroup = it->second;
 355
 356                         ofstream out;
 357                         m->openOutputFile(filename, out);
 358
 359                         for (map<string, string>::iterator itFile = nameMapForThisGroup.begin(); itFile != nameMapForThisGroup.end(); itFile++) {
 360
 361                                 if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
 362
 363                                 out << itFile->first << '\t' << itFile->second << endl;
 364                         }
 365
 366                         out.close();
 367                 }
 368
 369                 return 0;
 370         }
 371         catch(exception& e) {
 372                 m->errorOut(e, "SequenceParser", "getNameMap");
 373                 exit(1);
 374         }
 375 }
 376 /************************************************************/
 377
 378
 379