#include "decalc.h"
+//***************************************************************************************************************
+void DeCalculator::setMask(string m) {
+ try {
+ seqMask = m;
+
+ //whereever there is a base in the mask, save that value is query and subject
+ for (int i = 0; i < seqMask.length(); i++) {
+ if (isalpha(seqMask[i])) {
+ h.insert(i);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "setMask");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+void DeCalculator::runMask(Sequence* seq) {
+ try{
+
+ string q = seq->getAligned();
+ string tempQuery = "";
+
+ //whereever there is a base in the mask, save that value is query and subject
+ set<int>::iterator setit;
+ for ( setit=h.begin() ; setit != h.end(); setit++ ) {
+ tempQuery += q[*setit];
+ }
+
+ //save masked values
+ seq->setAligned(tempQuery);
+ seq->setUnaligned(tempQuery);
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "runMask");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+//num is query's spot in querySeqs
+void DeCalculator::trimSeqs(Sequence* query, Sequence subject, map<int, int>& trim) {
+ try {
+
+ string q = query->getAligned();
+ string s = subject.getAligned();
+
+ int front = 0;
+ for (int i = 0; i < q.length(); i++) {
+ if (isalpha(q[i]) && isalpha(s[i])) { front = i; break; }
+ }
+
+ int back = 0;
+ for (int i = q.length(); i >= 0; i--) {
+ if (isalpha(q[i]) && isalpha(s[i])) { back = i; break; }
+ }
+
+ trim[front] = back;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "trimSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+//find the window breaks for each sequence - this is so you can move ahead by bases.
+vector<int> DeCalculator::findWindows(Sequence* query, int front, int back, int& size, int increment) {
+ try {
+
+ vector<int> win;
+
+ int cutoff = back - front; //back - front
+
+ //if window is set to default
+ if (size == 0) { if (cutoff > 1200) { size = 300; }
+ else{ size = (cutoff / 4); } }
+ else if (size > (cutoff / 4)) {
+ mothurOut("You have selected to large a window size for sequence " + query->getName() + ". I will choose an appropriate window size."); mothurOutEndLine();
+ size = (cutoff / 4);
+ }
+
+ string seq = query->getAligned().substr(front, cutoff);
+
+ //count bases
+ int numBases = 0;
+ for (int l = 0; l < seq.length(); l++) { if (isalpha(seq[l])) { numBases++; } }
+
+ //save start of seq
+ win.push_back(front);
+
+ //move ahead increment bases at a time until all bases are in a window
+ int countBases = 0;
+ int totalBases = 0; //used to eliminate window of blanks at end of sequence
+
+ seq = query->getAligned();
+ for (int m = front; m < (back - size) ; m++) {
+
+ //count number of bases you see
+ if (isalpha(seq[m])) { countBases++; totalBases++; }
+
+ //if you have seen enough bases to make a new window
+ if (countBases >= increment) {
+ win.push_back(m); //save spot in alignment
+ countBases = 0; //reset bases you've seen in this window
+ }
+
+ //no need to continue if all your bases are in a window
+ if (totalBases == numBases) { break; }
+ }
+
+ return win;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "findWindows");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+vector<float> DeCalculator::calcObserved(Sequence* query, Sequence subject, vector<int> window, int size) {
+ try {
+
+ vector<float> temp;
+//cout << "query length = " << query->getAligned().length() << '\t' << " subject length = " << subject.getAligned().length() << endl;
+ for (int m = 0; m < window.size(); m++) {
+
+ string seqFrag = query->getAligned().substr(window[m], size);
+ string seqFragsub = subject.getAligned().substr(window[m], size);
+ //cout << "start point = " << window[m] << " end point = " << window[m]+size << endl;
+ int diff = 0;
+ for (int b = 0; b < seqFrag.length(); b++) {
+
+ if (seqFrag[b] != seqFragsub[b]) { diff++; }
+ }
+
+ //percentage of mismatched bases
+ float dist;
+ dist = diff / (float) seqFrag.length() * 100;
+
+ temp.push_back(dist);
+ }
+
+ return temp;
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "calcObserved");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+float DeCalculator::calcDist(Sequence* query, Sequence subject, int front, int back) {
+ try {
+
+ //so you only look at the trimmed part of the sequence
+ int cutoff = back - front;
+
+ //from first startpoint with length back-front
+ string seqFrag = query->getAligned().substr(front, cutoff);
+ string seqFragsub = subject.getAligned().substr(front, cutoff);
+
+ int diff = 0;
+ for (int b = 0; b < seqFrag.length(); b++) {
+ if (seqFrag[b] != seqFragsub[b]) { diff++; }
+ }
+
+ //percentage of mismatched bases
+ float dist = diff / (float) seqFrag.length() * 100;
+
+ return dist;
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "calcDist");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+vector<float> DeCalculator::calcExpected(vector<float> qav, float coef) {
+ try {
+
+ //for each window
+ vector<float> queryExpected;
+
+ for (int m = 0; m < qav.size(); m++) {
+
+ float expected = qav[m] * coef;
+
+ queryExpected.push_back(expected);
+ }
+
+ return queryExpected;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "calcExpected");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+float DeCalculator::calcDE(vector<float> obs, vector<float> exp) {
+ try {
+
+ //for each window
+ float sum = 0.0; //sum = sum from 1 to m of (oi-ei)^2
+ for (int m = 0; m < obs.size(); m++) { sum += ((obs[m] - exp[m]) * (obs[m] - exp[m])); }
+
+ float de = sqrt((sum / (obs.size() - 1)));
+
+ return de;
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "calcDE");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+vector<float> DeCalculator::calcFreq(vector<Sequence*> seqs, string filename) {
+ try {
+
+ vector<float> prob;
+ string freqfile = getRootName(filename) + "prob";
+ ofstream outFreq;
+
+ openOutputFile(freqfile, outFreq);
+
+ //at each position in the sequence
+ for (int i = 0; i < seqs[0]->getAligned().length(); i++) {
+
+ vector<int> freq; freq.resize(4,0);
+ int gaps = 0;
+
+ //find the frequency of each nucleotide
+ for (int j = 0; j < seqs.size(); j++) {
+
+ char value = seqs[j]->getAligned()[i];
+
+ if(toupper(value) == 'A') { freq[0]++; }
+ else if(toupper(value) == 'T' || toupper(value) == 'U') { freq[1]++; }
+ else if(toupper(value) == 'G') { freq[2]++; }
+ else if(toupper(value) == 'C') { freq[3]++; }
+ else { gaps++; }
+ }
+
+ //find base with highest frequency
+ int highest = 0;
+ for (int m = 0; m < freq.size(); m++) { if (freq[m] > highest) { highest = freq[m]; } }
+
+ float highFreq;
+ //subtract gaps to "ignore them"
+ if ( (seqs.size() - gaps) == 0 ) { highFreq = 1.0; }
+ else { highFreq = highest / (float) (seqs.size() - gaps); }
+
+ float Pi;
+ Pi = (highFreq - 0.25) / 0.75;
+
+ //cannot have probability less than 0.
+ if (Pi < 0) { Pi = 0.0; }
+
+ //saves this for later
+ outFreq << i+1 << '\t' << Pi << endl;
+
+ prob.push_back(Pi);
+ }
+
+ outFreq.close();
+
+ return prob;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "calcFreq");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<float> DeCalculator::findQav(vector<int> window, int size, vector<float> probabilityProfile) {
+ try {
+ vector<float> averages;
+
+ //for each window find average
+ for (int m = 0; m < window.size(); m++) {
+
+ float average = 0.0;
+
+ //while you are in the window for this sequence
+ int count = 0;
+ for (int j = window[m]; j < (window[m]+size); j++) {
+
+ //is this a spot that is included in the mask
+ if (h.count(j) > 0) {
+ average += probabilityProfile[j];
+ count++;
+ }
+ }
+
+ average = average / count;
+
+ //save this windows average
+ averages.push_back(average);
+ }
+
+ return averages;
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "findQav");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+vector< vector<float> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
+ try {
+ vector< vector<float> > quan;
+
+ //percentage of mismatched pairs 1 to 100
+ quan.resize(100);
+
+
+ //for each sequence
+ for(int i = start; i < end; i++){
+
+ mothurOut("Processing template sequence " + toString(i)); mothurOutEndLine();
+ Sequence* query = seqs[i];
+
+ //compare to every other sequence in template
+ for(int j = 0; j < i; j++){
+
+ Sequence subject = *(seqs[j]);
+
+ map<int, int> trim;
+ map<int, int>::iterator it;
+
+ trimSeqs(query, subject, trim);
+
+ it = trim.begin();
+ int front = it->first; int back = it->second;
+
+ //reset window for each new comparison
+ windowSizesTemplate[i] = window;
+
+ vector<int> win = findWindows(query, front, back, windowSizesTemplate[i], increment);
+
+ vector<float> obsi = calcObserved(query, subject, win, windowSizesTemplate[i]);
+
+ vector<float> q = findQav(win, windowSizesTemplate[i], probProfile);
+
+ float alpha = getCoef(obsi, q);
+
+ vector<float> exp = calcExpected(q, alpha);
+
+ float de = calcDE(obsi, exp);
+
+ float dist = calcDist(query, subject, front, back);
+
+ dist = ceil(dist);
+
+ //dist-1 because vector indexes start at 0.
+ quan[dist-1].push_back(de);
+
+ }
+ }
+
+ return quan;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "findQav");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+float DeCalculator::getCoef(vector<float> obs, vector<float> qav) {
+ try {
+
+ //find average prob for this seqs windows
+ float probAverage = 0.0;
+ for (int j = 0; j < qav.size(); j++) { probAverage += qav[j]; }
+ probAverage = probAverage / (float) qav.size();
+
+ //find observed average
+ float obsAverage = 0.0;
+ for (int j = 0; j < obs.size(); j++) { obsAverage += obs[j]; }
+ obsAverage = obsAverage / (float) obs.size();
+//cout << "sum ai / m = " << probAverage << endl;
+//cout << "sum oi / m = " << obsAverage << endl;
+ float coef = obsAverage / probAverage;
+
+ return coef;
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "getCoef");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+
projects / mothur.git / blobdiff