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/*
* qualityscores.cpp
* Mothur
*
* Created by Pat Schloss on 7/12/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "qualityscores.h"
/**************************************************************************************************/
QualityScores::QualityScores(){
try {
m = MothurOut::getInstance();
seqName = "";
seqLength = -1;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
exit(1);
}
}
/**************************************************************************************************/
QualityScores::QualityScores(ifstream& qFile){
try {
m = MothurOut::getInstance();
int score;
seqName = getSequenceName(qFile); m->gobble(qFile);
if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "'\n."); }
if (!m->control_pressed) {
string qScoreString = m->getline(qFile); m->gobble(qFile);
if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + qScoreString + "'\n."); }
while(qFile.peek() != '>' && qFile.peek() != EOF){
if (m->control_pressed) { break; }
string temp = m->getline(qFile); m->gobble(qFile);
//if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n."); }
qScoreString += ' ' + temp;
}
//cout << "done reading " << endl;
istringstream qScoreStringStream(qScoreString);
int count = 0;
while(!qScoreStringStream.eof()){
if (m->control_pressed) { break; }
string temp;
qScoreStringStream >> temp; m->gobble(qScoreStringStream);
//if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n."); }
//check temp to make sure its a number
if (!m->isContainingOnlyDigits(temp)) { m->mothurOut("[ERROR]: In sequence " + seqName + "'s quality scores, expected a number and got " + temp + ", setting score to 0."); m->mothurOutEndLine(); temp = "0"; }
convert(temp, score);
//cout << count << '\t' << score << endl;
qScores.push_back(score);
count++;
}
}
seqLength = qScores.size();
//cout << "seqlength = " << seqLength << endl;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
exit(1);
}
}
//********************************************************************************************************************
string QualityScores::getSequenceName(ifstream& qFile) {
try {
string name = "";
qFile >> name;
m->getline(qFile);
if (name.length() != 0) {
name = name.substr(1);
m->checkName(name);
}else{ m->mothurOut("Error in reading your qfile, at position " + toString(qFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true; }
return name;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "getSequenceName");
exit(1);
}
}
//********************************************************************************************************************
void QualityScores::setName(string name) {
try {
m->checkName(name);
seqName = name;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "setName");
exit(1);
}
}
/**************************************************************************************************/
string QualityScores::getName(){
try {
return seqName;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "getName");
exit(1);
}
}
/**************************************************************************************************/
void QualityScores::printQScores(ofstream& qFile){
try {
double aveQScore = calculateAverage(false);
qFile << '>' << seqName << '\t' << aveQScore << endl;
for(int i=0;i<seqLength;i++){
qFile << qScores[i] << ' ';
}
qFile << endl;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "printQScores");
exit(1);
}
}
/**************************************************************************************************/
void QualityScores::trimQScores(int start, int end){
try {
vector<int> hold;
//cout << seqName << '\t' << start << '\t' << end << '\t' << qScores.size() << endl;
//for (int i = 0; i < qScores.size(); i++) { cout << qScores[i] << end; }
if(end == -1){
hold = vector<int>(qScores.begin()+start, qScores.end());
qScores = hold;
}
if(start == -1){
if(qScores.size() > end){
hold = vector<int>(qScores.begin(), qScores.begin()+end);
qScores = hold;
}
}
seqLength = qScores.size();
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "trimQScores");
exit(1);
}
}
/**************************************************************************************************/
void QualityScores::flipQScores(){
try {
vector<int> temp = qScores;
for(int i=0;i<seqLength;i++){
qScores[seqLength - i - 1] = temp[i];
}
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "flipQScores");
exit(1);
}
}
/**************************************************************************************************/
bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
try {
string rawSequence = sequence.getUnaligned();
int seqLength = sequence.getNumBases();
if(seqName != sequence.getName()){
m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
m->mothurOutEndLine(); m->control_pressed = true;
}
int end;
for(int i=0;i<seqLength;i++){
end = i;
if(qScores[i] < qThreshold){
break;
}
}
//every score passed
if (end == (seqLength-1)) { end = seqLength; }
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
return 1;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "flipQScores");
exit(1);
}
}
/**************************************************************************************************/
bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshold, bool logTransform){
try {
string rawSequence = sequence.getUnaligned();
int seqLength = sequence.getNumBases();
if(seqName != sequence.getName()){
m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
m->mothurOutEndLine();
}
int end = -1;
double rollingSum = 0.0000;
double value = 0.0;
for(int i=0;i<seqLength;i++){
if (logTransform) {
rollingSum += (double)pow(10.0, qScores[i]);
value = log10(rollingSum / (double)(i+1));
} //Sum 10^Q
else {
rollingSum += (double)qScores[i];
value = rollingSum / (double)(i+1);
}
if(value < qThreshold){
end = i;
break;
}
}
if(end == -1){ end = seqLength; }
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
return 1;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "flipQScores");
exit(1);
}
}
/**************************************************************************************************/
bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int windowSize, double qThreshold, bool logTransform){
try {
string rawSequence = sequence.getUnaligned();
int seqLength = sequence.getNumBases();
if(seqName != sequence.getName()){
m->mothurOut("sequence name mismatch between fasta: " + sequence.getName() + " and qual file: " + seqName);
m->mothurOutEndLine();
}
int end = windowSize;
int start = 0;
if(seqLength < windowSize) { return 0; }
while((start+windowSize) < seqLength){
double windowSum = 0.0000;
for(int i=start;i<end;i++){
if (logTransform) { windowSum += pow(10.0, qScores[i]); }
else { windowSum += qScores[i]; }
}
double windowAverage = 0.0;
if (logTransform) { windowAverage = log10(windowSum / (double)(end-start)); }
else { windowAverage = windowSum / (double)(end-start); }
if(windowAverage < qThreshold){
end = end - stepSize;
break;
}
start += stepSize;
end = start + windowSize;
if(end >= seqLength){ end = seqLength; }
}
if(end == -1){ end = seqLength; }
//failed first window
if (end < windowSize) { return 0; }
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);
return 1;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "stripQualWindowAverage");
exit(1);
}
}
/**************************************************************************************************/
double QualityScores::calculateAverage(bool logTransform){
double aveQScore = 0.0000;
for(int i=0;i<seqLength;i++){
if (logTransform) { aveQScore += pow(10.0, qScores[i]); }
else { aveQScore += qScores[i]; }
}
aveQScore /= (double) seqLength;
if (logTransform) { aveQScore = log10(aveQScore /(double) seqLength); }
else { aveQScore /= (double) seqLength; }
return aveQScore;
}
/**************************************************************************************************/
bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage, bool logTransform){
try {
string rawSequence = sequence.getUnaligned();
bool success = 0; //guilty until proven innocent
if(seqName != sequence.getName()) {
m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
m->mothurOutEndLine();
}
double aveQScore = calculateAverage(logTransform);
if(aveQScore >= qAverage) { success = 1; }
else { success = 0; }
return success;
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "cullQualAverage");
exit(1);
}
}
/**************************************************************************************************/
void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap, string errorSeq, int start, int stop, int weight){
try {
int seqLength = errorSeq.size();
int qIndex = start - 1;
for(int i=0;i<seqLength;i++){
if(errorSeq[i] == 'm') { qualErrorMap['m'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 's') { qualErrorMap['s'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 'i') { qualErrorMap['i'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 'a') { qualErrorMap['a'][qScores[qIndex]] += weight; /*if(qScores[qIndex] != 0){ cout << qIndex << '\t'; }*/ }
else if(errorSeq[i] == 'd') { /* there are no qScores for deletions */ }
if(errorSeq[i] != 'd') { qIndex++; }
if(qIndex > stop){ break; }
}
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "updateQScoreErrorMap");
exit(1);
}
}
/**************************************************************************************************/
void QualityScores::updateForwardMap(vector<vector<int> >& forwardMap, int start, int stop, int weight){
try {
int index = 0;
for(int i=start-1;i<stop;i++){
forwardMap[index++][qScores[i]] += weight;
}
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "updateForwardMap");
exit(1);
}
}
/**************************************************************************************************/
void QualityScores::updateReverseMap(vector<vector<int> >& reverseMap, int start, int stop, int weight){
try {
int index = 0;
for(int i=stop-1;i>=start-1;i--){
reverseMap[index++][qScores[i]] += weight;
}
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "updateReverseMap");
exit(1);
}
}
/**************************************************************************************************/
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