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
  52 KmerDB::~KmerDB(){}
  53
  54 /**************************************************************************************************/
  55
  56 vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
  57         try {
  58                 vector<int> topMatches;
  59                 Kmer kmer(kmerSize);
  60                 searchScore = 0;
  61
  62                 vector<int> matches(numSeqs, 0);                                                //      a record of the sequences with shared kmers
  63                 vector<int> timesKmerFound(kmerLocations.size()+1, 0);  //      a record of the kmers that we have already found
  64
  65                 int numKmers = candidateSeq->getNumBases() - kmerSize + 1;
  66
  67                 for(int i=0;i<numKmers;i++){
  68                         int kmerNumber = kmer.getKmerNumber(candidateSeq->getUnaligned(), i);           //      go through the query sequence and get a kmer number
  69                         if(timesKmerFound[kmerNumber] == 0){                            //      if we haven't seen it before...
  70                                 for(int j=0;j<kmerLocations[kmerNumber].size();j++){//increase the count for each sequence that also has
  71                                         matches[kmerLocations[kmerNumber][j]]++;        //      that kmer
  72                                 }
  73                         }
  74                         timesKmerFound[kmerNumber] = 1;                                         //      ok, we've seen the kmer now
  75                 }
  76
  77                 vector<seqMatch> seqMatches;
  78                 for(int i=0;i<numSeqs;i++){
  79                         seqMatch temp(i, matches[i]);
  80                         seqMatches.push_back(temp);
  81                 }
  82
  83                 //sorts putting largest matches first
  84                 sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
  85
  86                 searchScore = seqMatches[0].match;
  87                 searchScore = 100 * searchScore / (float) numKmers;             //      return the Sequence object corresponding to the db
  88
  89                 //save top matches
  90                 for (int i = 0; i < num; i++) {
  91                         topMatches.push_back(seqMatches[i].seq);
  92                 }
  93
  94                 return topMatches;
  95         }
  96         catch(exception& e) {
  97                 m->errorOut(e, "KmerDB", "findClosestSequences");
  98                 exit(1);
  99         }
 100 }
 101
 102 /**************************************************************************************************/
 103
 104 void KmerDB::generateDB(){
 105         try {
 106
 107                 ofstream kmerFile;                                                                              //      once we have the kmerLocations folder print it out
 108                 openOutputFile(kmerDBName, kmerFile);                                   //      to a file
 109
 110                 for(int i=0;i<maxKmer;i++){                                                             //      step through all of the possible kmer numbers
 111                         kmerFile << i << ' ' << kmerLocations[i].size();        //      print the kmer number and the number of sequences with
 112                         for(int j=0;j<kmerLocations[i].size();j++){                     //      that kmer.  then print out the indices of the sequences
 113                                 kmerFile << ' ' << kmerLocations[i][j];                 //      with that kmer.
 114                         }
 115                         kmerFile << endl;
 116                 }
 117                 kmerFile.close();
 118
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "KmerDB", "generateDB");
 122                 exit(1);
 123         }
 124
 125 }
 126 /**************************************************************************************************/
 127 void KmerDB::addSequence(Sequence seq) {
 128         try {
 129                 Kmer kmer(kmerSize);
 130
 131                 string unaligned = seq.getUnaligned();  //      ...take the unaligned sequence...
 132                 int numKmers = unaligned.length() - kmerSize + 1;
 133
 134                 vector<int> seenBefore(maxKmer+1,0);
 135                 for(int j=0;j<numKmers;j++){                                            //      ...step though the sequence and get each kmer...
 136                         int kmerNumber = kmer.getKmerNumber(unaligned, j);
 137                         if(seenBefore[kmerNumber] == 0){
 138                                 kmerLocations[kmerNumber].push_back(count);             //      ...insert the sequence index into kmerLocations for
 139                         }                                                                                               //      the appropriate kmer number
 140                         seenBefore[kmerNumber] = 1;
 141                 }
 142
 143                 count++;
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "KmerDB", "addSequence");
 147                 exit(1);
 148         }
 149 }
 150 /**************************************************************************************************/
 151
 152 void KmerDB::readKmerDB(ifstream& kmerDBFile){
 153         try {
 154
 155                 kmerDBFile.seekg(0);                                                                    //      start at the beginning of the file
 156
 157                 string seqName;
 158                 int seqNumber;
 159
 160                 for(int i=0;i<maxKmer;i++){
 161                         int numValues = 0;
 162                         kmerDBFile >> seqName >> numValues;
 163
 164                         for(int j=0;j<numValues;j++){                                           //      for each kmer number get the...
 165                                 kmerDBFile >> seqNumber;                                                //              1. number of sequences with the kmer number
 166                                 kmerLocations[i].push_back(seqNumber);                  //              2. sequence indices
 167                         }
 168                 }
 169                 kmerDBFile.close();
 170
 171         }
 172         catch(exception& e) {
 173                 m->errorOut(e, "KmerDB", "readKmerDB");
 174                 exit(1);
 175         }
 176 }
 177
 178 /**************************************************************************************************/
 179 int KmerDB::getCount(int kmer) {
 180         try {
 181                 if (kmer < 0) { return 0; }  //if user gives negative number
 182                 else if (kmer > maxKmer) {      return 0;       }  //or a kmer that is bigger than maxkmer
 183                 else {  return kmerLocations[kmer].size();      }  // kmer is in vector range
 184         }
 185         catch(exception& e) {
 186                 m->errorOut(e, "KmerDB", "getCount");
 187                 exit(1);
 188         }
 189 }
 190 /**************************************************************************************************/
 191 vector<int> KmerDB::getSequencesWithKmer(int kmer) {
 192         try {
 193
 194                 vector<int> seqs;
 195
 196                 if (kmer < 0) { }  //if user gives negative number
 197                 else if (kmer > maxKmer) {      }  //or a kmer that is bigger than maxkmer
 198                 else {  seqs = kmerLocations[kmer];     }
 199
 200                 return seqs;
 201         }
 202         catch(exception& e) {
 203                 m->errorOut(e, "KmerDB", "getSequencesWithKmer");
 204                 exit(1);
 205         }
 206 }
 207
 208
 209 /**************************************************************************************************/
 210
 211