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/*
* alignNode.cpp
* bayesian
*
* Created by Pat Schloss on 10/11/11.
* Copyright 2011 Patrick D. Schloss. All rights reserved.
*
*/
#include "alignnode.h"
#include "taxonomynode.h"
#include "bayesian.h"
/**************************************************************************************************/
AlignNode::AlignNode(string n, int l): TaxonomyNode(n, l){
alignLength = 0;
}
/**************************************************************************************************/
void AlignNode::printTheta(){
try {
m->mothurOut("A:\t"); for(int i=0;i<alignLength;i++){ m->mothurOut(toString(theta[i].A)+ '\t'); } m->mothurOutEndLine();
m->mothurOut("T:\t"); for(int i=0;i<alignLength;i++){ m->mothurOut(toString(theta[i].T)+ '\t'); } m->mothurOutEndLine();
m->mothurOut("G:\t"); for(int i=0;i<alignLength;i++){ m->mothurOut(toString(theta[i].G)+ '\t'); } m->mothurOutEndLine();
m->mothurOut("C:\t"); for(int i=0;i<alignLength;i++){ m->mothurOut(toString(theta[i].C)+ '\t'); } m->mothurOutEndLine();
m->mothurOut("I:\t"); for(int i=0;i<alignLength;i++){ m->mothurOut(toString(theta[i].gap)+ '\t'); } m->mothurOutEndLine();
}
catch(exception& e) {
m->errorOut(e, "AlignNode", "printTheta");
exit(1);
}
}
/**************************************************************************************************/
int AlignNode::loadSequence(string& sequence){
try {
alignLength = (int)sequence.length(); // this function runs through the alignment and increments the frequency
// of each base for a particular taxon. we are building the thetas
if(theta.size() == 0){
theta.resize(alignLength);
columnCounts.resize(alignLength, 0);
}
for(int i=0;i<alignLength;i++){
if (m->getControl_pressed()) { return 0; }
char base = sequence[i];
if(base == 'A') { theta[i].A++; columnCounts[i]++; } // our thetas will be alignLength x 5
else if(base == 'T'){ theta[i].T++; columnCounts[i]++; } // and we ignore any position that has
else if(base == 'G'){ theta[i].G++; columnCounts[i]++; } // an ambiguous base call
else if(base == 'C'){ theta[i].C++; columnCounts[i]++; }
else if(base == '-'){ theta[i].gap++; columnCounts[i]++; }
else if(base == 'U'){ theta[i].T++; columnCounts[i]++; }
}
numSeqs++;
return 0;
}
catch(exception& e) {
m->errorOut(e, "AlignNode", "loadSequence");
exit(1);
}
}
/**************************************************************************************************/
int AlignNode::checkTheta(){
try {
for(int i=0;i<alignLength;i++){
if (m->getControl_pressed()) { return 0; }
if(theta[i].gap == columnCounts[i]){
columnCounts[i] = 0;
}
// else{
// int maxCount = theta[i].A;
//
// if(theta[i].T > maxCount) { maxCount = theta[i].T; }
// if(theta[i].G > maxCount) { maxCount = theta[i].T; }
// if(theta[i].C > maxCount) { maxCount = theta[i].T; }
// if(theta[i].gap > maxCount) { maxCount = theta[i].T; }
//
// if(maxCount < columnCounts[i] * 0.25){// || maxCount == columnCounts[i]){ //remove any column where the maximum frequency is <50%
// columnCounts[i] = 0;
// }
// }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "AlignNode", "checkTheta");
exit(1);
}
}
/**************************************************************************************************/
int AlignNode::addThetas(vector<thetaAlign> newTheta, int newNumSeqs){
try {
if(alignLength == 0){
alignLength = (int)newTheta.size();
theta.resize(alignLength);
columnCounts.resize(alignLength);
}
for(int i=0;i<alignLength;i++){
if (m->getControl_pressed()) { return 0; }
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;
return 0;
}
catch(exception& e) {
m->errorOut(e, "AlignNode", "addThetas");
exit(1);
}
}
/**************************************************************************************************/
double AlignNode::getSimToConsensus(string& query){
try {
double similarity = 0;
int length = 0;
for(int i=0;i<alignLength;i++){
if (m->getControl_pressed()) { return similarity; }
char base = query[i];
if(base != '.' && base != 'N' && columnCounts[i] != 0){
double fraction = 0;
if(base == 'A'){
fraction = (int) theta[i].A / (double) columnCounts[i];
similarity += fraction;
length++;
}
else if(base == 'T'){
fraction = (int) theta[i].T / (double) columnCounts[i];
similarity += fraction;
length++;
}
else if(base == 'G'){
fraction = (int) theta[i].G / (double) columnCounts[i];
similarity += fraction;
length++;
}
else if(base == 'C'){
fraction = (int) theta[i].C / (double) columnCounts[i];
similarity += fraction;
length++;
}
else if(base == '-'){
fraction = (int) theta[i].gap / (double) columnCounts[i];
similarity += fraction;
length++;
}
}
}
if(length != 0){
similarity /= double(length);
}
else {
similarity = 0;
}
return similarity;
}
catch(exception& e) {
m->errorOut(e, "AlignNode", "getSimToConsensus");
exit(1);
}
}
/**************************************************************************************************/
double AlignNode::getPxGivenkj_D_j(string& query){ //P(x | k_j, D, j)
try {
double PxGivenkj_D_j = 0;
int count = 0;
double alpha = 1 / (double)totalSeqs; //flat prior
for(int s=0;s<alignLength;s++){
if (m->getControl_pressed()) { return PxGivenkj_D_j; }
char base = query[s];
thetaAlign thetaS = theta[s];
if(base != '.' && base != 'N' && columnCounts[s] != 0){
double Nkj_s = (double)columnCounts[s];
double nkj_si = 0;
if(base == 'A') { nkj_si = (double)thetaS.A; }
else if(base == 'T'){ nkj_si = (double)thetaS.T; }
else if(base == 'G'){ nkj_si = (double)thetaS.G; }
else if(base == 'C'){ nkj_si = (double)thetaS.C; }
else if(base == '-'){ nkj_si = (double)thetaS.gap; }
else if(base == 'U'){ nkj_si = (double)thetaS.T; }
// double alpha = pow(0.2, double(Nkj_s)) + 0.0001; //need to make 1e-4 a variable in future; this is the non-flat prior
// if(columnCounts[s] != nkj_si){ //deal only with segregating sites...
double numerator = nkj_si + alpha;
double denomenator = Nkj_s + 5.0 * alpha;
PxGivenkj_D_j += log(numerator) - log(denomenator);
count++;
// }
}
if(base != '.' && columnCounts[s] == 0 && thetaS.gap == 0){
count = 0;
break;
}
}
if(count == 0){ PxGivenkj_D_j = -1e10; }
return PxGivenkj_D_j;
}
catch(exception& e) {
m->errorOut(e, "AlignNode", "getPxGivenkj_D_j");
exit(1);
}
}
/**************************************************************************************************/
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