/**************************************************************************************************/
-KmerDB::KmerDB(string fastaFileName, int kSize) : Database(fastaFileName), kmerSize(kSize) {
+KmerDB::KmerDB(string fastaFileName, int kSize) : Database(), kmerSize(kSize) {
try {
- string kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
- ifstream kmerFileTest(kmerDBName.c_str());
+ 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);
- if(!kmerFileTest){ // if we can open the kmer db file, then read it in...
- mothurOut("Generating the " + kmerDBName + " database...\t"); cout.flush();
- generateKmerDB(kmerDBName);
- }
- else{ // ...otherwise generate it.
- mothurOut("Reading in the " + kmerDBName + " database...\t"); cout.flush();
- readKmerDB(kmerDBName, kmerFileTest);
- }
- mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
-
}
catch(exception& e) {
- errorOut(e, "KmerDB", "KmerDB");
+ m->errorOut(e, "KmerDB", "KmerDB");
exit(1);
}
}
/**************************************************************************************************/
+KmerDB::KmerDB() : Database() {}
+/**************************************************************************************************/
-KmerDB::~KmerDB(){
-
- //for (int i = 0; i < templateSequences.size(); i++) { delete templateSequences[i]; }
- // templateSequences.clear();
-}
+KmerDB::~KmerDB(){}
/**************************************************************************************************/
-Sequence KmerDB::findClosestSequence(Sequence* candidateSeq){
+vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
try {
-
- Kmer kmer(kmerSize);
+ if (num > numSeqs) { m->mothurOut("[WARNING]: you requested " + toString(num) + " closest sequences, but the template only contains " + toString(numSeqs) + ", adjusting."); m->mothurOutEndLine(); num = numSeqs; }
+ vector<int> topMatches;
+ Kmer kmer(kmerSize);
searchScore = 0;
- int maxSequence = 0;
+ Scores.clear();
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...
timesKmerFound[kmerNumber] = 1; // ok, we've seen the kmer now
}
- for(int i=0;i<numSeqs;i++){ // find the db sequence that shares the most kmers with
- if(matches[i] > searchScore){ // the query sequence
- searchScore = 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);
}
-
- searchScore = 100 * searchScore / (float) numKmers; // return the Sequence object corresponding to the db
-
- return templateSequences[maxSequence]; // sequence with the most shared kmers.
-
+ return topMatches;
}
catch(exception& e) {
- errorOut(e, "KmerDB", "findClosestSequence");
+ m->errorOut(e, "KmerDB", "findClosestSequences");
exit(1);
}
}
/**************************************************************************************************/
-void KmerDB::generateKmerDB(string kmerDBName){
+void KmerDB::generateDB(){
try {
-
- Kmer kmer(kmerSize);
-
- for(int i=0;i<numSeqs;i++){ // for all of the template sequences...
-
- string seq = templateSequences[i].getUnaligned(); // ...take the unaligned sequence...
- int numKmers = seq.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(seq, j);
- if(seenBefore[kmerNumber] == 0){
- kmerLocations[kmerNumber].push_back(i); // ...insert the sequence index into kmerLocations for
- } // the appropriate kmer number
- seenBefore[kmerNumber] = 1;
- }
- }
ofstream kmerFile; // once we have the kmerLocations folder print it out
- openOutputFile(kmerDBName, kmerFile); // to a file
+ m->openOutputFile(kmerDBName, kmerFile); // to a file
+
+ //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
}
catch(exception& e) {
- errorOut(e, "KmerDB", "generateKmerDB");
+ m->errorOut(e, "KmerDB", "generateDB");
exit(1);
}
}
-
/**************************************************************************************************/
-
-void KmerDB::readKmerDB(string kmerDBName, ifstream& kmerDBFile){
+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++;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "addSequence");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+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;
+ int numValues = 0;
kmerDBFile >> seqName >> numValues;
for(int j=0;j<numValues;j++){ // for each kmer number get the...
}
catch(exception& e) {
- errorOut(e, "KmerDB", "readKmerDB");
+ m->errorOut(e, "KmerDB", "readKmerDB");
exit(1);
}
}
/**************************************************************************************************/
+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;
+
+ if (kmer < 0) { } //if user gives negative number
+ else if (kmer > maxKmer) { } //or a kmer that is bigger than maxkmer
+ else { seqs = kmerLocations[kmer]; }
+
+ return seqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KmerDB", "getSequencesWithKmer");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+
+/**************************************************************************************************/
+
+
projects / mothur.git / blobdiff