//***************************************************************************************************************
-Pintail::Pintail(string name) {
- try {
- fastafile = name;
- }
- catch(exception& e) {
- errorOut(e, "Pintail", "Pintail");
- exit(1);
- }
-}
+Pintail::Pintail(string filename, string temp) { fastafile = filename; templateFile = temp; }
//***************************************************************************************************************
Pintail::~Pintail() {
void Pintail::print(ostream& out) {
try {
- for (itCoef = DE.begin(); itCoef != DE.end(); itCoef++) {
+ for (int i = 0; i < querySeqs.size(); i++) {
+
+ int index = ceil(deviation[i]);
+
+ //is your DE value higher than the 95%
+ string chimera;
+ if (DE[i] > quantiles[index][4]) { chimera = "Yes"; }
+ else { chimera = "No"; }
- out << itCoef->first->getName() << '\t' << itCoef->second << endl;
+ out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl;
out << "Observed\t";
- itObsDist = obsDistance.find(itCoef->first);
- for (int i = 0; i < itObsDist->second.size(); i++) { out << itObsDist->second[i] << '\t'; }
+ for (int j = 0; j < obsDistance[i].size(); j++) { out << obsDistance[i][j] << '\t'; }
out << endl;
out << "Expected\t";
- itExpDist = expectedDistance.find(itCoef->first);
- for (int i = 0; i < itExpDist->second.size(); i++) { out << itExpDist->second[i] << '\t'; }
+ for (int m = 0; m < expectedDistance[i].size(); m++) { out << expectedDistance[i][m] << '\t'; }
out << endl;
}
-
-
}
catch(exception& e) {
errorOut(e, "Pintail", "print");
void Pintail::getChimeras() {
try {
- distCalculator = new ignoreGaps();
-
//read in query sequences and subject sequences
mothurOut("Reading sequences and template file... "); cout.flush();
querySeqs = readSeqs(fastafile);
int numSeqs = querySeqs.size();
- //if window is set to default
- if (window == 0) { if (querySeqs[0]->getAligned().length() > 800) { setWindow(200); }
- else{ setWindow((querySeqs[0]->getAligned().length() / 4)); } }
- else if (window > (querySeqs[0]->getAligned().length() / 4)) {
- mothurOut("You have selected to large a window size for you sequences. I will choose a smaller window."); mothurOutEndLine();
- setWindow((querySeqs[0]->getAligned().length() / 4));
- }
-
- //calculate number of iters
- iters = (querySeqs[0]->getAligned().length() - window + 1) / increment;
-cout << "length = " << querySeqs[0]->getAligned().length() << " window = " << window << " increment = " << increment << " iters = " << iters << endl;
+ obsDistance.resize(numSeqs);
+ expectedDistance.resize(numSeqs);
+ seqCoef.resize(numSeqs);
+ DE.resize(numSeqs);
+ Qav.resize(numSeqs);
+ bestfit.resize(numSeqs);
+ deviation.resize(numSeqs);
+ trimmed.resize(numSeqs);
+ windowSizes.resize(numSeqs, window);
+ windowSizesTemplate.resize(templateSeqs.size(), window);
+ windowsForeachQuery.resize(numSeqs);
+ quantiles.resize(100); //one for every percent mismatch
+
+ //break up file if needed
int linesPerProcess = processors / numSeqs;
- //find breakup of sequences for all times we will Parallelize
- if (processors == 1) { lines.push_back(new linePair(0, numSeqs)); }
- else {
- //fill line pairs
- for (int i = 0; i < (processors-1); i++) {
- lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess)));
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //find breakup of sequences for all times we will Parallelize
+ if (processors == 1) { lines.push_back(new linePair(0, numSeqs)); }
+ else {
+ //fill line pairs
+ for (int i = 0; i < (processors-1); i++) {
+ lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess)));
+ }
+ //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end
+ int i = processors - 1;
+ lines.push_back(new linePair((i*linesPerProcess), numSeqs));
}
- //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end
- int i = processors - 1;
- lines.push_back(new linePair((i*linesPerProcess), numSeqs));
- }
-
- //map query sequences to their most similiar sequences in the template - Parallelized
- mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
- if (processors == 1) { findPairs(lines[0]->start, lines[0]->end); }
- else { createProcessesPairs(); }
- mothurOut("Done."); mothurOutEndLine();
+
+ //find breakup of templatefile for quantiles
+ if (processors == 1) { templateLines.push_back(new linePair(0, templateSeqs.size())); }
+ else {
+ for (int i = 0; i < processors; i++) {
+ templateLines.push_back(new linePair());
+ templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size());
+ templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size());
+ }
+ }
+ #else
+ lines.push_back(new linePair(0, numSeqs));
+ templateLines.push_back(new linePair(0, templateSeqs.size()));
+ #endif
- //find Oqs for each sequence - the observed distance in each window - Parallelized
- mothurOut("Calculating observed percentage differences for each sequence... "); cout.flush();
- if (processors == 1) { calcObserved(lines[0]->start, lines[0]->end); }
- else { createProcessesObserved(); }
- mothurOut("Done."); mothurOutEndLine();
+ distcalculator = new ignoreGaps();
+
+
+ if (processors == 1) {
+ mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
+ bestfit = findPairs(lines[0]->start, lines[0]->end);
+
+ //ex.align matches from wigeon
+/*for (int m = 0; m < templateSeqs.size(); m++) {
+ if (templateSeqs[m]->getName() == "159481") { bestfit[17] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "100137") { bestfit[16] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "112956") { bestfit[15] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "102326") { bestfit[14] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "66229") { bestfit[13] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "206276") { bestfit[12] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "63607") { bestfit[11] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "7056") { bestfit[10] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "7088") { bestfit[9] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "17553") { bestfit[8] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "131723") { bestfit[7] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "69013") { bestfit[6] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "24543") { bestfit[5] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "27824") { bestfit[4] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "1456") { bestfit[3] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "1456") { bestfit[2] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "141312") { bestfit[1] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "141312") { bestfit[0] = *(templateSeqs[m]); }
+
+
+}*/
+
+ for (int j = 0; j < bestfit.size(); j++) {
+ //chops off beginning and end of sequences so they both start and end with a base
+ trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+ mothurOut("Finding window breaks... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ it = trimmed[i].begin();
+cout << "trimmed = " << it->first << '\t' << it->second << endl;
+ vector<int> win = findWindows(querySeqs[i], it->first, it->second, windowSizes[i]);
+ windowsForeachQuery[i] = win;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+ }else { createProcessesSpots(); }
+
//find P
- mothurOut("Calculating expected percentage differences for each sequence... "); cout.flush();
- vector<float> probabilityProfile = calcFreq(templateSeqs);
+ mothurOut("Getting conservation... "); cout.flush();
+ if (consfile == "") {
+ mothurOut("Calculating probability of conservation for your template sequences. This can take a while... I will output the quantiles to a .prob file so that you can input them using the conservation parameter next time you run this command. Providing the .prob file will dramatically improve speed. "); cout.flush();
+ probabilityProfile = calcFreq(templateSeqs);
+ mothurOut("Done."); mothurOutEndLine();
+ }else { probabilityProfile = readFreq(); }
//make P into Q
for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; }
-
- //find Qav
- averageProbability = findQav(probabilityProfile);
-
- //find Coefficient - maps a sequence to its coefficient
- seqCoef = getCoef(averageProbability);
-
- //find Eqs for each sequence - the expected distance in each window - Parallelized
- if (processors == 1) { calcExpected(lines[0]->start, lines[0]->end); }
- else { createProcessesExpected(); }
mothurOut("Done."); mothurOutEndLine();
- //find deviation - Parallelized
- mothurOut("Finding deviation from expected... "); cout.flush();
- if (processors == 1) { calcDE(lines[0]->start, lines[0]->end); }
- else { createProcessesDE(); }
- mothurOut("Done."); mothurOutEndLine();
+ if (processors == 1) {
+
+ mothurOut("Calculating observed distance... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ cout << querySeqs[i]->getName() << '\t' << bestfit[i].getName() << " windows = " << windowsForeachQuery[i].size() << " size = " << windowSizes[i] << endl;
+ vector<float> obsi = calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
+ obsDistance[i] = obsi;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+ mothurOut("Finding variability... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> q = findQav(windowsForeachQuery[i], windowSizes[i]);
+ Qav[i] = q;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+ mothurOut("Calculating alpha... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ float alpha = getCoef(obsDistance[i], Qav[i]);
+ seqCoef.push_back(alpha);
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+ mothurOut("Calculating expected distance... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> exp = calcExpected(Qav[i], seqCoef[i]);
+ expectedDistance[i] = exp;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+ mothurOut("Finding deviation... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ float de = calcDE(obsDistance[i], expectedDistance[i]);
+ DE[i] = de;
- //free memory
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; }
- delete distCalculator;
+ it = trimmed[i].begin();
+ float dist = calcDist(querySeqs[i], bestfit[i], it->first, it->second);
+ deviation[i] = dist;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+ }
+ else { createProcesses(); }
+
+
+ //quantiles are used to determine whether the de values found indicate a chimera
+ //if you have to calculate them, its time intensive because you are finding the de and deviation values for each
+ //combination of sequences in the template
+ if (quanfile != "") { quantiles = readQuantiles(); }
+ else {
+
+ mothurOut("Calculating quantiles for your template. This can take a while... I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command. Providing the .quan file will dramatically improve speed. "); cout.flush();
+ if (processors == 1) {
+ quantiles = getQuantiles(0, templateSeqs.size());
+ }else { createProcessesQuan(); }
+
+ ofstream out4;
+ string o = getRootName(templateFile) + "quan";
+
+ openOutputFile(o, out4);
+
+ //adjust quantiles
+ for (int i = 0; i < quantiles.size(); i++) {
+ if (quantiles[i].size() == 0) {
+ //in case this is not a distance found in your template files
+ for (int g = 0; g < 6; g++) {
+ quantiles[i].push_back(0.0);
+ }
+ }else{
+
+ sort(quantiles[i].begin(), quantiles[i].end());
+
+ vector<float> temp;
+ //save 10%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.10)]);
+ //save 25%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.25)]);
+ //save 50%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.5)]);
+ //save 75%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.75)]);
+ //save 95%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.95)]);
+ //save 99%
+ temp.push_back(quantiles[i][int(quantiles[i].size() * 0.99)]);
+
+ quantiles[i] = temp;
+ }
+
+ //output quan value
+ out4 << i+1 << '\t';
+ for (int u = 0; u < quantiles[i].size(); u++) { out4 << quantiles[i][u] << '\t'; }
+ out4 << endl;
+ }
+
+ mothurOut("Done."); mothurOutEndLine();
+ }
+
+ //free memory
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; }
+ for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i]; }
+
+ delete distcalculator;
}
catch(exception& e) {
errorOut(e, "Pintail", "getChimeras");
exit(1);
}
}
+//***************************************************************************************************************
+//num is query's spot in querySeqs
+void Pintail::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, "Pintail", "trimSeqs");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-vector<Sequence*> Pintail::readSeqs(string file) {
+vector<float> Pintail::readFreq() {
try {
ifstream in;
- openInputFile(file, in);
- vector<Sequence*> container;
+ openInputFile(consfile, in);
+
+ vector<float> prob;
+
+ //read in probabilities and store in vector
+ int pos; float num;
- //read in seqs and store in vector
while(!in.eof()){
- Sequence* current = new Sequence(in);
- if (current->getAligned() == "") { current->setAligned(current->getUnaligned()); }
- //takes out stuff is needed
- current->setUnaligned(current->getUnaligned());
+ in >> pos >> num;
- container.push_back(current);
+ //do you want this spot
+ prob.push_back(num);
gobble(in);
}
in.close();
- return container;
+ return prob;
}
catch(exception& e) {
- errorOut(e, "Pintail", "readSeqs");
+ errorOut(e, "Pintail", "readFreq");
exit(1);
}
}
+//***************************************************************************************************************
+
+vector< vector<float> > Pintail::readQuantiles() {
+ try {
+
+ ifstream in;
+ openInputFile(quanfile, in);
+
+ vector< vector<float> > quan;
+
+ int num; float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
+
+ while(!in.eof()){
+
+ in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
+
+ vector <float> temp;
+
+ temp.push_back(ten);
+ temp.push_back(twentyfive);
+ temp.push_back(fifty);
+ temp.push_back(seventyfive);
+ temp.push_back(ninetyfive);
+ temp.push_back(ninetynine);
+
+ quan.push_back(temp);
+
+ gobble(in);
+ }
+
+ in.close();
+ return quan;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Pintail", "readQuantiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
//calculate the distances from each query sequence to all sequences in the template to find the closest sequence
-void Pintail::findPairs(int start, int end) {
+vector<Sequence> Pintail::findPairs(int start, int end) {
try {
+ vector<Sequence> seqsMatches; seqsMatches.resize(end-start);
+
for(int i = start; i < end; i++){
float smallest = 10000.0;
Sequence temp = *(templateSeqs[j]);
- distCalculator->calcDist(query, temp);
- float dist = distCalculator->getDist();
+ distcalculator->calcDist(query, temp);
+ float dist = distcalculator->getDist();
if (dist < smallest) {
-
- bestfit[querySeqs[i]] = templateSeqs[j];
+ seqsMatches[i] = *(templateSeqs[j]);
smallest = dist;
}
}
}
+ return seqsMatches;
+
}
catch(exception& e) {
errorOut(e, "Pintail", "findPairs");
exit(1);
}
}
+
//***************************************************************************************************************
-void Pintail::calcObserved(int start, int end) {
+//find the window breaks for each sequence - this is so you can move ahead by bases.
+vector<int> Pintail::findWindows(Sequence* query, int front, int back, int& size) {
try {
-
-
- for(int i = start; i < end; i++){
- itBest = bestfit.find(querySeqs[i]);
- Sequence* query;
- Sequence* subject;
+ vector<int> win;
- if (itBest != bestfit.end()) {
- query = itBest->first;
- subject = itBest->second;
- }else{ mothurOut("Error in calcObserved"); mothurOutEndLine(); }
-//cout << query->getName() << '\t' << subject->getName() << endl;
+ int cutoff = back - front; //back - front
- int startpoint = 0;
- for (int m = 0; m < iters; m++) {
-
- string seqFrag = query->getAligned().substr(startpoint, window);
- string seqFragsub = subject->getAligned().substr(startpoint, window);
-
- int diff = 0;
- for (int b = 0; b < seqFrag.length(); b++) {
-
- //if this is not a gap
- if ((isalpha(seqFrag[b])) && (isalpha(seqFragsub[b]))) {
- //and they are different - penalize
- if (seqFrag[b] != seqFragsub[b]) { diff++; }
- }
- }
-
- //percentage of mismatched bases
- float dist = diff / (float)seqFrag.length();
+ //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++) {
- obsDistance[query].push_back(dist);
+ //count number of bases you see
+ if (isalpha(seq[m])) { countBases++; totalBases++; }
- startpoint += increment;
+ //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, "Pintail", "calcObserved");
+ errorOut(e, "Pintail", "findWindows");
exit(1);
}
}
//***************************************************************************************************************
-void Pintail::calcExpected(int start, int end) {
+vector<float> Pintail::calcObserved(Sequence* query, Sequence subject, vector<int> window, int size) {
try {
-
- //for each sequence
- for(int i = start; i < end; i++){
-
- itCoef = seqCoef.find(querySeqs[i]);
- float coef = itCoef->second;
-
- //for each window
- vector<float> queryExpected;
- for (int m = 0; m < iters; m++) {
- float expected = averageProbability[m] * coef;
- queryExpected.push_back(expected);
-//cout << "average variabilty over window = " << averageProbability[m] << " coef = " << coef << " ei = " << expected << '\t' << "window = " << m << endl;
+ 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);
+ }
- expectedDistance[querySeqs[i]] = queryExpected;
+ return temp;
+ }
+ catch(exception& e) {
+ errorOut(e, "Pintail", "calcObserved");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+float Pintail::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, "Pintail", "calcExpected");
+ errorOut(e, "Pintail", "calcDist");
exit(1);
}
}
+
//***************************************************************************************************************
-void Pintail::calcDE(int start, int end) {
+vector<float> Pintail::calcExpected(vector<float> qav, float coef) {
try {
-
- //for each sequence
- for(int i = start; i < end; i++){
+ //for each window
+ vector<float> queryExpected;
- itObsDist = obsDistance.find(querySeqs[i]);
- vector<float> obs = itObsDist->second;
+ for (int m = 0; m < qav.size(); m++) {
+
+ float expected = qav[m] * coef;
+
+ queryExpected.push_back(expected);
+ }
- itExpDist = expectedDistance.find(querySeqs[i]);
- vector<float> exp = itExpDist->second;
-// cout << "difference between obs and exp = " << abs(obs[m] - exp[m]) << endl;
- //for each window
- float sum = 0.0; //sum = sum from 1 to m of (oi-ei)^2
- for (int m = 0; m < iters; m++) { sum += ((obs[m] - exp[m]) * (obs[m] - exp[m])); }
+ return queryExpected;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Pintail", "calcExpected");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+float Pintail::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 / (iters - 1)));
+ float de = sqrt((sum / (obs.size() - 1)));
- DE[querySeqs[i]] = de;
- }
-
+ return de;
}
catch(exception& e) {
errorOut(e, "Pintail", "calcDE");
try {
vector<float> prob;
+ string freqfile = getRootName(templateFile) + "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;
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]++; }
//find base with highest frequency
int highest = 0;
- for (int m = 0; m < freq.size(); m++) { if (freq[m] > highest) { highest = freq[m]; } }
+ 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;
- //add in gaps - so you can effectively "ignore them"
- highest += gaps;
+ //cannot have probability less than 0.
+ if (Pi < 0) { Pi = 0.0; }
- float highFreq = highest / (float) seqs.size();
+ //saves this for later
+ outFreq << i+1 << '\t' << Pi << endl;
- float Pi;
- Pi = (highFreq - 0.25) / 0.75;
-
prob.push_back(Pi);
}
+ outFreq.close();
+
return prob;
}
}
}
//***************************************************************************************************************
-vector<float> Pintail::findQav(vector<float> prob) {
+vector<float> Pintail::findQav(vector<int> window, int size) {
try {
- vector<float> averages;
-
+ vector<float> averages;
+
//for each window find average
- int startpoint = 0;
- for (int m = 0; m < iters; m++) {
-
+ for (int m = 0; m < window.size(); m++) {
+
float average = 0.0;
- for (int i = startpoint; i < (startpoint+window); i++) { average += prob[i]; }
-
- average = average / window;
-//cout << average << endl;
+
+ //while you are in the window for this sequence
+ for (int j = window[m]; j < (window[m]+size); j++) { average += probabilityProfile[j]; }
+
+ average = average / size;
+
//save this windows average
averages.push_back(average);
-
- startpoint += increment;
}
-
+
return averages;
}
catch(exception& e) {
exit(1);
}
}
+
//***************************************************************************************************************
-map<Sequence*, float> Pintail::getCoef(vector<float> prob) {
+vector< vector<float> > Pintail::getQuantiles(int start, int end) {
try {
- map<Sequence*, float> coefs;
+ vector< vector<float> > quan;
- //find average prob
- float probAverage = 0.0;
- for (int i = 0; i < prob.size(); i++) { probAverage += prob[i]; }
- probAverage = probAverage / (float) prob.size();
-cout << "(sum of ai) / m = " << probAverage << endl;
- //find a coef for each sequence
- map<Sequence*, vector<float> >::iterator it;
- for (it = obsDistance.begin(); it != obsDistance.end(); it++) {
-
- vector<float> temp = it->second;
- Sequence* tempSeq = it->first;
-
- //find observed average
- float obsAverage = 0.0;
- for (int i = 0; i < temp.size(); i++) { obsAverage += temp[i]; }
- obsAverage = obsAverage / (float) temp.size();
-cout << tempSeq->getName() << '\t' << obsAverage << endl;
- float coef = obsAverage / probAverage;
-cout << tempSeq->getName() << '\t' << "coef = " << coef << endl;
- //save this sequences coefficient
- coefs[tempSeq] = coef;
- }
+ //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 = templateSeqs[i];
+
+ //compare to every other sequence in template
+ for(int j = 0; j < i; j++){
+
+ Sequence subject = *(templateSeqs[j]);
+
+ map<int, int> trim;
+ 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]);
+
+ vector<float> obsi = calcObserved(query, subject, win, windowSizesTemplate[i]);
+
+ vector<float> q = findQav(win, windowSizesTemplate[i]);
+
+ 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;
- return coefs;
}
catch(exception& e) {
- errorOut(e, "Pintail", "getCoef");
+ errorOut(e, "Pintail", "findQav");
exit(1);
}
}
-/**************************************************************************************************/
-
-void Pintail::createProcessesPairs() {
+//***************************************************************************************************************
+float Pintail::getCoef(vector<float> obs, vector<float> qav) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
- vector<int> processIDS;
+
+ //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();
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid);
- process++;
- }else if (pid == 0){
- findPairs(lines[process]->start, lines[process]->end);
- exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
- }
+ //find observed average
+ float obsAverage = 0.0;
+ for (int j = 0; j < obs.size(); j++) { obsAverage += obs[j]; }
+ obsAverage = obsAverage / (float) obs.size();
- //force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
-#else
- findPairs(lines[0]->start, lines[0]->end);
-#endif
+ float coef = obsAverage / probAverage;
+
+ return coef;
}
catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesPairs");
+ errorOut(e, "Pintail", "getCoef");
exit(1);
}
}
-
/**************************************************************************************************/
-void Pintail::createProcessesObserved() {
+void Pintail::createProcessesSpots() {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
vector<int> processIDS;
+ vector< vector<int> > win; win.resize(querySeqs.size());
//loop through and create all the processes you want
while (process != processors) {
processIDS.push_back(pid);
process++;
}else if (pid == 0){
- calcObserved(lines[process]->start, lines[process]->end);
+
+ mothurOut("Finding pairs for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
+ vector<Sequence> tempbest;
+ tempbest = findPairs(lines[process]->start, lines[process]->end);
+ int count = 0;
+ for (int i = lines[process]->start; i < lines[process]->end; i++) {
+ bestfit[i] = tempbest[count];
+
+ //chops off beginning and end of sequences so they both start and end with a base
+ trimSeqs(querySeqs[i], bestfit[i], trimmed[i]);
+ count++;
+ }
+ mothurOut("Done finding pairs for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
+
+ mothurOut("Finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
+ for (int i = lines[process]->start; i < lines[process]->end; i++) {
+ vector<int> temp = findWindows(querySeqs[i], it->first, it->second, windowSizes[i]);
+ win[i] = temp;
+ }
+ mothurOut("Done finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
+
exit(0);
}else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
}
wait(&temp);
}
+ windowsForeachQuery = win;
#else
- calcObserved(lines[0]->start, lines[0]->end);
+ bestfit = findPairs(lines[0]->start, lines[0]->end);
+ for (int j = 0; j < bestfit.size(); j++) {
+ //chops off beginning and end of sequences so they both start and end with a base
+ trimSeqs(querySeqs[j], bestfit[j], j);
+ }
+
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ it = trimmed[i].begin();
+ map<int, int> win = findWindows(querySeqs[i], it->first, it->second, windowSizes[i]);
+ windows[i] = win;
+ }
#endif
}
catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesObserved");
+ errorOut(e, "Pintail", "createProcessesSpots");
exit(1);
}
}
-//***************************************************************************************************************
-void Pintail::createProcessesExpected() {
+/**************************************************************************************************/
+
+void Pintail::createProcesses() {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
vector<int> processIDS;
+ vector< vector<float> > exp; exp.resize(querySeqs.size());
+ vector<float> de; de.resize(querySeqs.size());
+ vector< vector<float> > obs; obs.resize(querySeqs.size());
+ vector<float> dev; dev.resize(querySeqs.size());
+
+
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
processIDS.push_back(pid);
process++;
}else if (pid == 0){
- calcExpected(lines[process]->start, lines[process]->end);
+
+ mothurOut("Calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
+ for (int i = lines[process]->start; i < lines[process]->end; i++) {
+
+ vector<float> obsi = calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
+ obs[i] = obsi;
+
+ //calc Qav
+ vector<float> q = findQav(windowsForeachQuery[i], windowSizes[i]);
+
+ //get alpha
+ float alpha = getCoef(obsDistance[i], q);
+
+ //find expected
+ vector<float> exp = calcExpected(q, alpha);
+ expectedDistance[i] = exp;
+
+ //get de and deviation
+ float dei = calcDE(obsi, exp);
+ de[i] = dei;
+
+ it = trimmed[i].begin();
+ float dist = calcDist(querySeqs[i], bestfit[i], it->first, it->second);
+ dev[i] = dist;
+ }
+ mothurOut("Done calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
+
exit(0);
}else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
}
wait(&temp);
}
+ obsDistance = obs;
+ expectedDistance = exp;
+ DE = de;
+ deviation = dev;
+
#else
- calcExpected(lines[0]->start, lines[0]->end);
+ mothurOut("Calculating observed distance... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> obsi = calcObserved(querySeqs[i], bestfit[i], windows[i], windowSizes[i]);
+ obsDistance[i] = obsi;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Finding variability... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> q = findQav(windows[i], windowSizes[i]);
+ Qav[i] = q;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Calculating alpha... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ float alpha = getCoef(obsDistance[i], Qav[i]);
+ seqCoef.push_back(alpha);
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Calculating expected distance... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ vector<float> exp = calcExpected(Qav[i], seqCoef[i]);
+ expectedDistance[i] = exp;
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+
+
+ mothurOut("Finding deviation... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ float de = calcDE(obsDistance[i], expectedDistance[i]);
+ DE[i] = de;
+
+ it = trimmed[i].begin();
+ float dist = calcDist(querySeqs[i], bestfit[i], it->first, it->second);
+ deviation[i] = dist;
+ }
+ mothurOut("Done."); mothurOutEndLine();
#endif
}
catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesExpected");
+ errorOut(e, "Pintail", "createProcesses");
exit(1);
}
}
+
/**************************************************************************************************/
-void Pintail::createProcessesDE() {
+void Pintail::createProcessesQuan() {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
vector<int> processIDS;
-
+ vector< vector<float> > quan; quan.resize(100);
+
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
processIDS.push_back(pid);
process++;
}else if (pid == 0){
- calcDE(lines[process]->start, lines[process]->end);
+
+ vector< vector<float> > q = getQuantiles(templateLines[process]->start, templateLines[process]->end);
+
+ for (int i = 0; i < q.size(); i++) {
+ //put all values of q[i] into quan[i]
+ quan[i].insert(quan[i].begin(), q[i].begin(), q[i].end());
+ }
+
+ for (int i = 0; i < quan.size(); i++) {
+ cout << i+1 << '\t';
+ for (int j = 0; j < quan[i].size(); j++) { cout << quan[i][j] << '\t'; }
+ cout << endl;
+ }
+
exit(0);
}else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
}
wait(&temp);
}
+ quantiles = quan;
#else
- calcDE(lines[0]->start, lines[0]->end);
-
+ quantiles = getQuantiles(0, templateSeqs.size());
#endif
}
catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesDE");
+ errorOut(e, "Pintail", "createProcessesQuan");
exit(1);
}
}
+
//***************************************************************************************************************
projects / mothur.git / blobdiff