* Created by Pat Schloss on 12/16/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
- */
-
-using namespace std;
+ * This class is a child class of the Database class, which stores the template sequences as a kmer table and provides
+ * a method of searching the kmer table for the sequence with the most kmers in common with a query sequence.
+ * kmerLocations is the primary storage variable that is a two-dimensional vector where each row represents the
+ * different number of kmers and each column contains the index to sequences that use that kmer.
+ *
+ * Construction of an object of this type will first look for an appropriately named database file and if it is found
+ * then will read in the database file (readKmerDB), otherwise it will generate one and store the data in memory
+ * (generateKmerDB)
+ *
+ * The search method used here is roughly the same as that used in the SimRank program that is found at the
+ * greengenes website. The default kmer size is 7. The speed complexity is between O(L) and O(LN). When I use 7mers
+ * on average a kmer is found in ~100 other sequences with a database of ~5000 sequences. If this is the case then the
+ * time would be on the order of O(0.1LN) -> fast.
+ *
+ */
#include "sequence.hpp"
#include "kmer.hpp"
/**************************************************************************************************/
-KmerDB::KmerDB(string fastaFileName, int kSize) : Database(fastaFileName), kmerSize(kSize) {
-
- string kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
- ifstream kmerFileTest(kmerDBName.c_str());
-
- int power4s[9] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536 };
+KmerDB::KmerDB(string fastaFileName, int kSize) : Database(), kmerSize(kSize) {
+ try {
- maxKmer = power4s[kmerSize];
- kmerLocations.resize(maxKmer+1);
-
- if(!kmerFileTest){
- cout << "Generating the " << kmerDBName << " database...\t"; cout.flush();
- generateKmerDB(kmerDBName);
- }
- else{
- cout << "Reading in the " << kmerDBName << " database...\t"; cout.flush();
- readKmerDB(kmerDBName, kmerFileTest);
+ kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+
+ int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
+ count = 0;
+
+ maxKmer = power4s[kmerSize];
+ kmerLocations.resize(maxKmer+1);
+
}
- cout << "DONE." << endl << endl; cout.flush();
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "KmerDB");
+ exit(1);
+ }
}
+/**************************************************************************************************/
+KmerDB::KmerDB() : Database() {}
+/**************************************************************************************************/
+
+KmerDB::~KmerDB(){}
/**************************************************************************************************/
-Sequence* KmerDB::findClosestSequence(Sequence* candidateSeq){
-
- vector<int> matches(numSeqs, 0);
- vector<int> timesKmerFound(kmerLocations.size()+1, 0);
-
- int maxMatches = 0;
- int maxSequence = 0;
-
- string query = candidateSeq->getUnaligned();
-
- int numKmers = query.length() - kmerSize + 1;
- Kmer kmer(kmerSize);
-
- for(int i=0;i<numKmers;i++){
+vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
+ try {
+ if (num > numSeqs) { m->mothurOut("[WARNING]: you requested " + toString(num) + " closest sequences, but the template only contains " + toString(numSeqs) + ", adjusting."); m->mothurOutEndLine(); num = numSeqs; }
- int kmerNumber = kmer.getKmerNumber(query, i);
+ vector<int> topMatches;
+ Kmer kmer(kmerSize);
+ searchScore = 0;
+ Scores.clear();
- if(timesKmerFound[kmerNumber] == 0){
- for(int j=0;j<kmerLocations[kmerNumber].size();j++){
- matches[kmerLocations[kmerNumber][j]]++;
+ vector<int> matches(numSeqs, 0); // a record of the sequences with shared kmers
+ vector<int> timesKmerFound(kmerLocations.size()+1, 0); // a record of the kmers that we have already found
+
+ int numKmers = candidateSeq->getNumBases() - kmerSize + 1;
+
+ for(int i=0;i<numKmers;i++){
+ int kmerNumber = kmer.getKmerNumber(candidateSeq->getUnaligned(), i); // go through the query sequence and get a kmer number
+ if(timesKmerFound[kmerNumber] == 0){ // if we haven't seen it before...
+ for(int j=0;j<kmerLocations[kmerNumber].size();j++){//increase the count for each sequence that also has
+ matches[kmerLocations[kmerNumber][j]]++; // that kmer
+ }
}
+ timesKmerFound[kmerNumber] = 1; // ok, we've seen the kmer now
}
- timesKmerFound[kmerNumber] = 1;
- }
- for(int i=0;i<numSeqs;i++){
- if(matches[i] > maxMatches){
- maxMatches = matches[i];
- maxSequence = i;
+ if (num != 1) {
+ vector<seqMatch> seqMatches; seqMatches.resize(numSeqs);
+ for(int i=0;i<numSeqs;i++){
+ seqMatches[i].seq = i;
+ seqMatches[i].match = matches[i];
+ }
+
+ //sorts putting largest matches first
+ sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
+
+ searchScore = seqMatches[0].match;
+ searchScore = 100 * searchScore / (float) numKmers; // return the Sequence object corresponding to the db
+
+ //save top matches
+ for (int i = 0; i < num; i++) {
+ topMatches.push_back(seqMatches[i].seq);
+ float thisScore = 100 * seqMatches[i].match / (float) numKmers;
+ Scores.push_back(thisScore);
+ }
+ }else{
+ int bestIndex = 0;
+ int bestMatch = -1;
+ for(int i=0;i<numSeqs;i++){
+
+ if (matches[i] > bestMatch) {
+ bestIndex = i;
+ bestMatch = matches[i];
+ }
+ }
+
+ searchScore = bestMatch;
+ searchScore = 100 * searchScore / (float) numKmers; // return the Sequence object corresponding to the db
+ topMatches.push_back(bestIndex);
+ Scores.push_back(searchScore);
}
+ return topMatches;
}
- return templateSequences[maxSequence];
-
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "findClosestSequences");
+ exit(1);
+ }
}
/**************************************************************************************************/
-void KmerDB::generateKmerDB(string kmerDBName){
-
-
- Kmer kmer(kmerSize);
-
- for(int i=0;i<numSeqs;i++){
-
- string seq = templateSequences[i]->getUnaligned();
- int numKmers = seq.length() - kmerSize + 1;
+void KmerDB::generateDB(){
+ try {
+
+ ofstream kmerFile; // once we have the kmerLocations folder print it out
+ m->openOutputFile(kmerDBName, kmerFile); // to a file
- for(int j=0;j<numKmers;j++){
- int kmerNumber = kmer.getKmerNumber(seq, j);
- kmerLocations[kmerNumber].push_back(i);
+ //output version
+ kmerFile << "#" << m->getVersion() << endl;
+
+ for(int i=0;i<maxKmer;i++){ // step through all of the possible kmer numbers
+ kmerFile << i << ' ' << kmerLocations[i].size(); // print the kmer number and the number of sequences with
+ for(int j=0;j<kmerLocations[i].size();j++){ // that kmer. then print out the indices of the sequences
+ kmerFile << ' ' << kmerLocations[i][j]; // with that kmer.
+ }
+ kmerFile << endl;
}
+ kmerFile.close();
+
}
-
- ofstream kmerFile(kmerDBName.c_str(), ios::trunc);
- if(!kmerFile) {
- cerr << "Error: Could not open " << kmerDBName << endl;
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "generateDB");
exit(1);
- }
+ }
- for(int i=0;i<maxKmer;i++){
- kmerFile << i << ' ' << kmerLocations[i].size();
- for(int j=0;j<kmerLocations[i].size();j++){
- kmerFile << ' ' << kmerLocations[i][j];
- }
- kmerFile << endl;
+}
+/**************************************************************************************************/
+void KmerDB::addSequence(Sequence seq) {
+ try {
+ Kmer kmer(kmerSize);
+
+ string unaligned = seq.getUnaligned(); // ...take the unaligned sequence...
+ int numKmers = unaligned.length() - kmerSize + 1;
+
+ vector<int> seenBefore(maxKmer+1,0);
+ for(int j=0;j<numKmers;j++){ // ...step though the sequence and get each kmer...
+ int kmerNumber = kmer.getKmerNumber(unaligned, j);
+ if(seenBefore[kmerNumber] == 0){
+ kmerLocations[kmerNumber].push_back(count); // ...insert the sequence index into kmerLocations for
+ } // the appropriate kmer number
+ seenBefore[kmerNumber] = 1;
+ }
+
+ count++;
}
- kmerFile.close();
-
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "addSequence");
+ exit(1);
+ }
}
-
/**************************************************************************************************/
-void KmerDB::readKmerDB(string kmerDBName, ifstream& kmerDBFile){
+void KmerDB::readKmerDB(ifstream& kmerDBFile){
+ try {
+
+ kmerDBFile.seekg(0); // start at the beginning of the file
+
+ //read version
+ string line = m->getline(kmerDBFile); m->gobble(kmerDBFile);
+
+ string seqName;
+ int seqNumber;
+
+ for(int i=0;i<maxKmer;i++){
+ int numValues = 0;
+ kmerDBFile >> seqName >> numValues;
+
+ for(int j=0;j<numValues;j++){ // for each kmer number get the...
+ kmerDBFile >> seqNumber; // 1. number of sequences with the kmer number
+ kmerLocations[i].push_back(seqNumber); // 2. sequence indices
+ }
+ }
+ kmerDBFile.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "readKmerDB");
+ exit(1);
+ }
+}
- kmerDBFile.seekg(0);
-
- string seqName;
- int seqNumber;
+/**************************************************************************************************/
+int KmerDB::getCount(int kmer) {
+ try {
+ if (kmer < 0) { return 0; } //if user gives negative number
+ else if (kmer > maxKmer) { return 0; } //or a kmer that is bigger than maxkmer
+ else { return kmerLocations[kmer].size(); } // kmer is in vector range
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "getCount");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int KmerDB::getReversed(int kmerNumber) {
+ try {
+ Kmer kmer(kmerSize);
+
+ if (kmerNumber < 0) { return 0; } //if user gives negative number
+ else if (kmerNumber > maxKmer) { return 0; } //or a kmer that is bigger than maxkmer
+ else { return kmer.getReverseKmerNumber(kmerNumber); } // kmer is in vector range
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "getReversed");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<int> KmerDB::getSequencesWithKmer(int kmer) {
+ try {
+
+ vector<int> seqs;
- for(int i=0;i<numSeqs;i++){
- int numValues;
- kmerDBFile >> seqName >> numValues;
+ if (kmer < 0) { } //if user gives negative number
+ else if (kmer > maxKmer) { } //or a kmer that is bigger than maxkmer
+ else { seqs = kmerLocations[kmer]; }
- for(int j=0;j<numValues;j++){
- kmerDBFile >> seqNumber;
- kmerLocations[i].push_back(seqNumber);
- }
+ return seqs;
}
- kmerDBFile.close();
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "getSequencesWithKmer");
+ exit(1);
+ }
}
+/**************************************************************************************************/
+
/**************************************************************************************************/
+
+
projects / mothur.git / blobdiff