#include "decalc.h"
+//***************************************************************************************************************
+void DeCalculator::setMask(string m) {
+ try {
+ seqMask = m;
+
+ if (seqMask.length() != 0) {
+ //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);
+ }
+ }
+ }else {
+ for (int i = 0; i < alignLength; 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++) {
+//cout << "query = " << q[i] << " subject = " << s[i] << endl;
+ if (isalpha(q[i]) && isalpha(s[i])) { front = i; break; }
+ }
+//cout << endl << endl;
+ int back = 0;
+ for (int i = q.length(); i >= 0; i--) {
+//cout << "query = " << q[i] << " subject = " << s[i] << endl;
+ if (isalpha(q[i]) && isalpha(s[i])) { back = i; break; }
+ }
+
+ trim[front] = back;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "trimSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+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++; } }
+//cout << "num Bases = " << numBases << endl;
+ //save start of seq
+ win.push_back(front);
+//cout << front << '\t';
+ //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++; }
+
+ //if you have seen enough bases to make a new window
+ if (countBases >= increment) {
+ //total bases is the number of bases in a window already.
+ totalBases += countBases;
+//cout << "total bases = " << totalBases << endl;
+ win.push_back(m); //save spot in alignment
+//cout << m << '\t';
+ 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; }
+ }
+
+
+ //get last window if needed
+ if (totalBases < numBases) { win.push_back(back-size); }
+//cout << endl << endl;
+*/
+
+ //this follows wigeon, but we may want to consider that it chops off the end values if the sequence cannot be evenly divided into steps
+ for (int m = front; m < (back - size) ; m+=increment) { win.push_back(m); }
+
+
+
+ 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;
+ //int gaps = 0;
+ for (int m = 0; m < window.size(); m++) {
+
+ string seqFrag = query->getAligned().substr(window[m], size);
+ string seqFragsub = subject->getAligned().substr(window[m], size);
+
+ int diff = 0;
+ for (int b = 0; b < seqFrag.length(); b++) {
+ //if at least one is a base and they are not equal
+ if( (isalpha(seqFrag[b]) || isalpha(seqFragsub[b])) && (seqFrag[b] != seqFragsub[b]) ) { diff++; }
+
+ //ignore gaps
+ //if((!isalpha(seqFrag[b])) && (!isalpha(seqFragsub[b]))) { gaps++; }
+ }
+
+ //percentage of mismatched bases
+ float dist;
+
+ //if the whole fragment is 0 distance = 0
+ //if ((seqFrag.length()-gaps) == 0) { dist = 0.0; }
+
+ //percentage of mismatched bases
+ //else { dist = diff / (float) (seqFrag.length()-gaps) * 100; }
+
+ 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;
+ int gaps = 0;
+
+ //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++) {
+ //ignore gaps
+ if((!isalpha(seqFrag[b])) && (!isalpha(seqFragsub[b]))) { gaps++; }
+ if (seqFrag[b] != seqFragsub[b]) { diff++; }
+ }
+
+ //if the whole fragment is 0 distance = 0
+ if ((seqFrag.length()-gaps) == 0) { return 0.0; }
+
+ //percentage of mismatched bases
+ float dist = diff / (float) (seqFrag.length()-gaps) * 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
+ int numZeros = 0;
+ for (int m = 0; m < obs.size(); m++) {
+
+ //if (obs[m] != 0.0) {
+ sum += ((obs[m] - exp[m]) * (obs[m] - exp[m]));
+ //}else { numZeros++; }
+
+ }
+
+ float de = sqrt((sum / (obs.size() - 1 - numZeros)));
+
+ 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) + "freq";
+ ofstream outFreq;
+
+ openOutputFile(freqfile, outFreq);
+
+ string length = toString(seqs.size()); //if there are 5000 seqs in the template then set precision to 3
+ int precision = length.length() - 1;
+
+ //format output
+ outFreq.setf(ios::fixed, ios::floatfield); outFreq.setf(ios::showpoint);
+
+ //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 = highest / (float) (seqs.size());
+
+ 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 << setprecision(precision) << i << '\t' << highFreq << endl;
+
+ if (h.count(i) > 0) {
+ 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++) {
+ 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);
+ }
+}
+//***************************************************************************************************************
+//seqs have already been masked
+vector< vector<quanMember> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
+ try {
+ vector< vector<quanMember> > quan;
+
+ //percentage of mismatched pairs 1 to 100
+ quan.resize(100);
+//ofstream o;
+//string out = "getQuantiles.out";
+//openOutputFile(out, o);
+
+ //for each sequence
+ for(int i = start; i < end; i++){
+
+ mothurOut("Processing sequence " + toString(i)); mothurOutEndLine();
+ Sequence* query = new Sequence(seqs[i]->getName(), seqs[i]->getAligned());
+
+ //compare to every other sequence in template
+ for(int j = 0; j < i; j++){
+
+ Sequence* subject = new Sequence(seqs[j]->getName(), seqs[j]->getAligned());
+
+ 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);
+ //o << i << '\t' << j << '\t' << dist << '\t' << de << endl;
+ dist = ceil(dist);
+
+ quanMember newScore(de, i, j);
+
+ //dist-1 because vector indexes start at 0.
+ quan[dist-1].push_back(newScore);
+
+ delete subject;
+ }
+
+ delete query;
+ }
+
+ return quan;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "getQuantiles");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareQuanMembers(quanMember left, quanMember right){
+ return (left.score < right.score);
+}
+//***************************************************************************************************************
+//this was going to be used by pintail to increase the sensitivity of the chimera detection, but it wasn't quite right. may want to revisit in the future...
+void DeCalculator::removeObviousOutliers(vector< vector<quanMember> >& quantiles, int num) {
+ try {
+
+ for (int i = 0; i < quantiles.size(); i++) {
+
+ //find mean of this quantile score
+ sort(quantiles[i].begin(), quantiles[i].end(), compareQuanMembers);
+
+ float high = quantiles[i][int(quantiles[i].size() * 0.99)].score;
+ float low = quantiles[i][int(quantiles[i].size() * 0.01)].score;
+
+ vector<quanMember> temp;
+
+ //look at each value in quantiles to see if it is an outlier
+ for (int j = 0; j < quantiles[i].size(); j++) {
+ //is this score between 1 and 99%
+ if ((quantiles[i][j].score > low) && (quantiles[i][j].score < high)) {
+ temp.push_back(quantiles[i][j]);
+ }
+ }
+
+ quantiles[i] = temp;
+ }
+
+/*
+ //find contributer with most offending score related to it
+ int largestContrib = findLargestContrib(seen);
+
+ //while you still have guys to eliminate
+ while (contributions.size() > 0) {
+
+ mothurOut("Removing scores contributed by sequence " + toString(largestContrib) + " in your template file."); mothurOutEndLine();
+
+ //remove from quantiles all scores that were made using this largestContrib
+ for (int i = 0; i < quantiles.size(); i++) {
+//cout << "before remove " << quantiles[i].size() << '\t';
+ removeContrib(largestContrib, quantiles[i]);
+//cout << "after remove " << quantiles[i].size() << endl;
+ }
+//cout << count << " largest contrib = " << largestContrib << endl; count++;
+ //remove from contributions all scores that were made using this largestContrib
+ removeContrib(largestContrib, contributions);
+
+ //"erase" largestContrib
+ seen[largestContrib] = -1;
+
+ //get next largestContrib
+ largestContrib = findLargestContrib(seen);
+ }
+ABOVE IS ATTEMPT #1
+**************************************************************************************************
+BELOW IS ATTEMPT #2
+ vector<int> marked = returnObviousOutliers(quantiles, num);
+ vector<int> copyMarked = marked;
+
+ //find the 99% of marked
+ sort(copyMarked.begin(), copyMarked.end());
+ int high = copyMarked[int(copyMarked.size() * 0.99)];
+cout << "high = " << high << endl;
+
+ for(int i = 0; i < marked.size(); i++) {
+ if (marked[i] > high) {
+ mothurOut("Removing scores contributed by sequence " + toString(marked[i]) + " in your template file."); mothurOutEndLine();
+ for (int i = 0; i < quantiles.size(); i++) {
+ removeContrib(marked[i], quantiles[i]);
+ }
+ }
+
+ }
+
+
+ //adjust quantiles
+ for (int i = 0; i < quantiles.size(); i++) {
+ vector<float> temp;
+
+ if (quantiles[i].size() == 0) {
+ //in case this is not a distance found in your template files
+ for (int g = 0; g < 6; g++) {
+ temp.push_back(0.0);
+ }
+ }else{
+
+ sort(quantiles[i].begin(), quantiles[i].end(), compareQuanMembers);
+
+ //save 10%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.10)].score);
+ //save 25%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.25)].score);
+ //save 50%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.5)].score);
+ //save 75%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.75)].score);
+ //save 95%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.95)].score);
+ //save 99%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.99)].score);
+
+ }
+
+ quan[i] = temp;
+
+ }
+*/
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "removeObviousOutliers");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+//put quanMember in the vector based on how far they are from the 99% or 1%. Biggest offenders in front.
+/*vector<quanMember> DeCalculator::sortContrib(map<quanMember*, float> quan) {
+ try{
+
+ vector<quanMember> newQuan;
+ map<quanMember*, float>::iterator it;
+
+ while (quan.size() > 0) {
+
+ map<quanMember*, float>::iterator largest = quan.begin();
+
+ //find biggest member
+ for (it = quan.begin(); it != quan.end(); it++) {
+ if (it->second > largest->second) { largest = it; }
+ }
+cout << largest->second << '\t' << largest->first->score << '\t' << largest->first->member1 << '\t' << largest->first->member2 << endl;
+ //save it
+ newQuan.push_back(*(largest->first));
+
+ //erase from quan
+ quan.erase(largest);
+ }
+
+ return newQuan;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "sortContrib");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+//used by removeObviousOutliers which was attempt to increase sensitivity of chimera detection...not currently used...
+int DeCalculator::findLargestContrib(vector<int> seen) {
+ try{
+
+ int largest = 0;
+
+ int largestContribs;
+
+ for (int i = 0; i < seen.size(); i++) {
+
+ if (seen[i] > largest) {
+ largestContribs = i;
+ largest = seen[i];
+ }
+ }
+
+ return largestContribs;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "findLargestContribs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+void DeCalculator::removeContrib(int bad, vector<quanMember>& quan) {
+ try{
+
+ vector<quanMember> newQuan;
+ for (int i = 0; i < quan.size(); i++) {
+ if ((quan[i].member1 != bad) && (quan[i].member2 != bad) ) {
+ newQuan.push_back(quan[i]);
+ }
+ }
+
+ quan = newQuan;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "removeContrib");
+ exit(1);
+ }
+}
+*/
+//***************************************************************************************************************
+float DeCalculator::findAverage(vector<float> myVector) {
+ try{
+
+ float total = 0.0;
+ for (int i = 0; i < myVector.size(); i++) { total += myVector[i]; }
+
+ float average = total / (float) myVector.size();
+
+ return average;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "findAverage");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+float DeCalculator::getCoef(vector<float> obs, vector<float> qav) {
+ try {
+
+ //find average prob for this seqs windows
+ float probAverage = findAverage(qav);
+
+ //find observed average
+ float obsAverage = findAverage(obs);
+
+ float coef = obsAverage / probAverage;
+
+ return coef;
+ }
+ catch(exception& e) {
+ errorOut(e, "DeCalculator", "getCoef");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+
projects / mothur.git / blobdiff