kmerdb.cpp

   1 /*
   2  *  kmerdb.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/16/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  *      This class is a child class of the Database class, which stores the template sequences as a kmer table and provides
   9  *      a method of searching the kmer table for the sequence with the most kmers in common with a query sequence.
  10  *      kmerLocations is the primary storage variable that is a two-dimensional vector where each row represents the
  11  *      different number of kmers and each column contains the index to sequences that use that kmer.
  12  *
  13  *      Construction of an object of this type will first look for an appropriately named database file and if it is found
  14  *      then will read in the database file (readKmerDB), otherwise it will generate one and store the data in memory
  15  *      (generateKmerDB)
  16  *
  17  *      The search method used here is roughly the same as that used in the SimRank program that is found at the
  18  *      greengenes website.  The default kmer size is 7.  The speed complexity is between O(L) and O(LN).  When I use 7mers
  19  *      on average a kmer is found in ~100 other sequences with a database of ~5000 sequences.  If this is the case then the
  20  *      time would be on the order of O(0.1LN) -> fast.
  21  *
  22
  23  */
  24
  25 #include "sequence.hpp"
  26 #include "kmer.hpp"
  27 #include "database.hpp"
  28 #include "kmerdb.hpp"
  29
  30 /**************************************************************************************************/
  31
  32 KmerDB::KmerDB(string fastaFileName, int kSize) : Database(), kmerSize(kSize) {
  33         try {
  34
  35                 kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
  36
  37                 int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
  38                 count = 0;
  39
  40                 maxKmer = power4s[kmerSize];
  41                 kmerLocations.resize(maxKmer+1);
  42
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "KmerDB", "KmerDB");
  46                 exit(1);
  47         }
  48
  49 }
  50 /**************************************************************************************************/
  51 KmerDB::KmerDB() : Database() {}
  52 /**************************************************************************************************/
  53
  54 KmerDB::~KmerDB(){}
  55
  56 /**************************************************************************************************/
  57
  58 vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
  59         try {
  60                 vector<int> topMatches;
  61                 Kmer kmer(kmerSize);
  62                 searchScore = 0;
  63                 Scores.clear();
  64
  65                 vector<int> matches(numSeqs, 0);                                                //      a record of the sequences with shared kmers
  66                 vector<int> timesKmerFound(kmerLocations.size()+1, 0);  //      a record of the kmers that we have already found
  67
  68                 int numKmers = candidateSeq->getNumBases() - kmerSize + 1;
  69
  70                 for(int i=0;i<numKmers;i++){
  71                         int kmerNumber = kmer.getKmerNumber(candidateSeq->getUnaligned(), i);           //      go through the query sequence and get a kmer number
  72                         if(timesKmerFound[kmerNumber] == 0){                            //      if we haven't seen it before...
  73                                 for(int j=0;j<kmerLocations[kmerNumber].size();j++){//increase the count for each sequence that also has
  74                                         matches[kmerLocations[kmerNumber][j]]++;        //      that kmer
  75                                 }
  76                         }
  77                         timesKmerFound[kmerNumber] = 1;                                         //      ok, we've seen the kmer now
  78                 }
  79
  80                 if (num != 1) {
  81                         vector<seqMatch> seqMatches; seqMatches.resize(numSeqs);
  82                         for(int i=0;i<numSeqs;i++){
  83                                 seqMatches[i].seq = i;
  84                                 seqMatches[i].match = matches[i];
  85                         }
  86
  87                         //sorts putting largest matches first
  88                         sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
  89
  90                         searchScore = seqMatches[0].match;
  91                         searchScore = 100 * searchScore / (float) numKmers;             //      return the Sequence object corresponding to the db
  92
  93                         //save top matches
  94                         for (int i = 0; i < num; i++) {
  95                                 topMatches.push_back(seqMatches[i].seq);
  96                                 float thisScore = 100 * seqMatches[i].match / (float) numKmers;
  97                                 Scores.push_back(thisScore);
  98                         }
  99                 }else{
 100                         int bestIndex = 0;
 101                         int bestMatch = -1;
 102                         for(int i=0;i<numSeqs;i++){
 103
 104                                 if (matches[i] > bestMatch) {
 105                                         bestIndex = i;
 106                                         bestMatch = matches[i];
 107                                 }
 108                         }
 109
 110                         searchScore = bestMatch;
 111                         searchScore = 100 * searchScore / (float) numKmers;             //      return the Sequence object corresponding to the db
 112                         topMatches.push_back(bestIndex);
 113                         Scores.push_back(searchScore);
 114                 }
 115                 return topMatches;
 116         }
 117         catch(exception& e) {
 118                 m->errorOut(e, "KmerDB", "findClosestSequences");
 119                 exit(1);
 120         }
 121 }
 122
 123 /**************************************************************************************************/
 124
 125 void KmerDB::generateDB(){
 126         try {
 127
 128                 ofstream kmerFile;                                                                              //      once we have the kmerLocations folder print it out
 129                 m->openOutputFile(kmerDBName, kmerFile);                                        //      to a file
 130
 131                 //output version
 132                 kmerFile << "#" << m->getVersion() << endl;
 133
 134                 for(int i=0;i<maxKmer;i++){                                                             //      step through all of the possible kmer numbers
 135                         kmerFile << i << ' ' << kmerLocations[i].size();        //      print the kmer number and the number of sequences with
 136                         for(int j=0;j<kmerLocations[i].size();j++){                     //      that kmer.  then print out the indices of the sequences
 137                                 kmerFile << ' ' << kmerLocations[i][j];                 //      with that kmer.
 138                         }
 139                         kmerFile << endl;
 140                 }
 141                 kmerFile.close();
 142
 143         }
 144         catch(exception& e) {
 145                 m->errorOut(e, "KmerDB", "generateDB");
 146                 exit(1);
 147         }
 148
 149 }
 150 /**************************************************************************************************/
 151 void KmerDB::addSequence(Sequence seq) {
 152         try {
 153                 Kmer kmer(kmerSize);
 154
 155                 string unaligned = seq.getUnaligned();  //      ...take the unaligned sequence...
 156                 int numKmers = unaligned.length() - kmerSize + 1;
 157
 158                 vector<int> seenBefore(maxKmer+1,0);
 159                 for(int j=0;j<numKmers;j++){                                            //      ...step though the sequence and get each kmer...
 160                         int kmerNumber = kmer.getKmerNumber(unaligned, j);
 161                         if(seenBefore[kmerNumber] == 0){
 162                                 kmerLocations[kmerNumber].push_back(count);             //      ...insert the sequence index into kmerLocations for
 163                         }                                                                                               //      the appropriate kmer number
 164                         seenBefore[kmerNumber] = 1;
 165                 }
 166
 167                 count++;
 168         }
 169         catch(exception& e) {
 170                 m->errorOut(e, "KmerDB", "addSequence");
 171                 exit(1);
 172         }
 173 }
 174 /**************************************************************************************************/
 175
 176 void KmerDB::readKmerDB(ifstream& kmerDBFile){
 177         try {
 178
 179                 kmerDBFile.seekg(0);                                                                    //      start at the beginning of the file
 180
 181                 //read version
 182                 string line = m->getline(kmerDBFile); m->gobble(kmerDBFile);
 183
 184                 string seqName;
 185                 int seqNumber;
 186
 187                 for(int i=0;i<maxKmer;i++){
 188                         int numValues = 0;
 189                         kmerDBFile >> seqName >> numValues;
 190
 191                         for(int j=0;j<numValues;j++){                                           //      for each kmer number get the...
 192                                 kmerDBFile >> seqNumber;                                                //              1. number of sequences with the kmer number
 193                                 kmerLocations[i].push_back(seqNumber);                  //              2. sequence indices
 194                         }
 195                 }
 196                 kmerDBFile.close();
 197
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "KmerDB", "readKmerDB");
 201                 exit(1);
 202         }
 203 }
 204
 205 /**************************************************************************************************/
 206 int KmerDB::getCount(int kmer) {
 207         try {
 208                 if (kmer < 0) { return 0; }  //if user gives negative number
 209                 else if (kmer > maxKmer) {      return 0;       }  //or a kmer that is bigger than maxkmer
 210                 else {  return kmerLocations[kmer].size();      }  // kmer is in vector range
 211         }
 212         catch(exception& e) {
 213                 m->errorOut(e, "KmerDB", "getCount");
 214                 exit(1);
 215         }
 216 }
 217 /**************************************************************************************************/
 218 vector<int> KmerDB::getSequencesWithKmer(int kmer) {
 219         try {
 220
 221                 vector<int> seqs;
 222
 223                 if (kmer < 0) { }  //if user gives negative number
 224                 else if (kmer > maxKmer) {      }  //or a kmer that is bigger than maxkmer
 225                 else {  seqs = kmerLocations[kmer];     }
 226
 227                 return seqs;
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "KmerDB", "getSequencesWithKmer");
 231                 exit(1);
 232         }
 233 }
 234 /**************************************************************************************************/
 235
 236
 237 /**************************************************************************************************/
 238
 239