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/*
* kmerNode.cpp
* bayesian
*
* Created by Pat Schloss on 10/11/11.
* Copyright 2011 Patrick D. Schloss. All rights reserved.
*
*/
#include "kmernode.h"
/**********************************************************************************************************************/
KmerNode::KmerNode(string s, int l, int n) : TaxonomyNode(s, l), kmerSize(n) {
try {
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
numPossibleKmers = power4s[kmerSize];
numUniqueKmers = 0;
kmerVector.assign(numPossibleKmers, 0);
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "KmerNode");
exit(1);
}
}
/**********************************************************************************************************************/
void KmerNode::loadSequence(vector<int>& kmerProfile){
try {
for(int i=0;i<numPossibleKmers;i++){
if (m->control_pressed) { break; }
if(kmerVector[i] == 0 && kmerProfile[i] != 0) { numUniqueKmers++; }
kmerVector[i] += kmerProfile[i];
}
numSeqs++;
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "loadSequence");
exit(1);
}
}
/**********************************************************************************************************************/
string KmerNode::getKmerBases(int kmerNumber){
try {
// Here we convert the kmer number into the kmer in terms of bases.
//
// Example: Score = 915 (for a 6-mer)
// Base6 = (915 / 4^0) % 4 = 915 % 4 = 3 => T [T]
// Base5 = (915 / 4^1) % 4 = 228 % 4 = 0 => A [AT]
// Base4 = (915 / 4^2) % 4 = 57 % 4 = 1 => C [CAT]
// Base3 = (915 / 4^3) % 4 = 14 % 4 = 2 => G [GCAT]
// Base2 = (915 / 4^4) % 4 = 3 % 4 = 3 => T [TGCAT]
// Base1 = (915 / 4^5) % 4 = 0 % 4 = 0 => A [ATGCAT] -> this checks out with the previous method
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
string kmer = "";
if(kmerNumber == power4s[kmerSize]){//pow(4.,7)){ // if the kmer number is the same as the maxKmer then it must
for(int i=0;i<kmerSize;i++){ // have had an N in it and so we'll just call it N x kmerSize
kmer += 'N';
}
}
else{
for(int i=0;i<kmerSize;i++){
if (m->control_pressed) { return kmer; }
int nt = (int)(kmerNumber / (float)power4s[i]) % 4; // the '%' operator returns the remainder
if(nt == 0) { kmer = 'A' + kmer; } // from int-based division ]
else if(nt == 1){ kmer = 'C' + kmer; }
else if(nt == 2){ kmer = 'G' + kmer; }
else if(nt == 3){ kmer = 'T' + kmer; }
}
}
return kmer;
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "getKmerBases");
exit(1);
}
}
/**************************************************************************************************/
void KmerNode::addThetas(vector<int> newTheta, int newNumSeqs){
try {
for(int i=0;i<numPossibleKmers;i++){
if (m->control_pressed) { break; }
kmerVector[i] += newTheta[i];
}
// if(alignLength == 0){
// alignLength = (int)newTheta.size();
// theta.resize(alignLength);
// columnCounts.resize(alignLength);
// }
//
// for(int i=0;i<alignLength;i++){
// theta[i].A += newTheta[i].A; columnCounts[i] += newTheta[i].A;
// theta[i].T += newTheta[i].T; columnCounts[i] += newTheta[i].T;
// theta[i].G += newTheta[i].G; columnCounts[i] += newTheta[i].G;
// theta[i].C += newTheta[i].C; columnCounts[i] += newTheta[i].C;
// theta[i].gap += newTheta[i].gap; columnCounts[i] += newTheta[i].gap;
// }
numSeqs += newNumSeqs;
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "addThetas");
exit(1);
}
}
/**********************************************************************************************************************/
int KmerNode::getNumUniqueKmers(){
try {
if(numUniqueKmers == 0){
for(int i=0;i<numPossibleKmers;i++){
if (m->control_pressed) { return numUniqueKmers; }
if(kmerVector[i] != 0){
numUniqueKmers++;
}
}
}
return numUniqueKmers;
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "getNumUniqueKmers");
exit(1);
}
}
/**********************************************************************************************************************/
void KmerNode::printTheta(){
try {
m->mothurOut(name + "\n");
for(int i=0;i<numPossibleKmers;i++){
if(kmerVector[i] != 0){
m->mothurOut(getKmerBases(i) + '\t' + toString(kmerVector[i]) + "\n");
}
}
m->mothurOutEndLine();
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "printTheta");
exit(1);
}
}
/**************************************************************************************************/
double KmerNode::getSimToConsensus(vector<int>& queryKmerProfile){
try {
double present = 0;
for(int i=0;i<numPossibleKmers;i++){
if (m->control_pressed) { return present; }
if(queryKmerProfile[i] != 0 && kmerVector[i] != 0){
present++;
}
}
return present / double(queryKmerProfile.size() - kmerSize + 1);
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "getSimToConsensus");
exit(1);
}
}
/**********************************************************************************************************************/
double KmerNode::getPxGivenkj_D_j(vector<int>& queryKmerProfile) {
try {
double sumLogProb = 0.0000;
double alpha = 1.0 / (double)totalSeqs; //flat prior
// double alpha = pow((1.0 / (double)numUniqueKmers), numSeqs)+0.0001; //non-flat prior
for(int i=0;i<numPossibleKmers;i++){
if (m->control_pressed) { return sumLogProb; }
if(queryKmerProfile[i] != 0){ //numUniqueKmers needs to be the value from Root;
sumLogProb += log((kmerVector[i] + alpha) / (numSeqs + numUniqueKmers * alpha));
}
}
return sumLogProb;
}
catch(exception& e) {
m->errorOut(e, "KmerNode", "getPxGivenkj_D_j");
exit(1);
}
}
/**********************************************************************************************************************/
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