#include "pintail.h"
#include "ignoregaps.h"
+#include "eachgapdist.h"
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareQuanMembers(quanMember left, quanMember right){
+ return (left.score < right.score);
+}
//***************************************************************************************************************
-Pintail::Pintail(string filename, string temp) { fastafile = filename; templateFile = temp; }
+Pintail::Pintail(string filename, string o) {
+ fastafile = filename; outputDir = o;
+ distcalculator = new eachGapDist();
+ decalc = new DeCalculator();
+}
//***************************************************************************************************************
Pintail::~Pintail() {
try {
- for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; }
- for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; }
- if (processors != 1) { for (int i = 0; i < bestfit.size(); i++) { delete bestfit[i]; } }
+ delete distcalculator;
+ delete decalc;
}
catch(exception& e) {
errorOut(e, "Pintail", "~Pintail");
exit(1);
}
-}
-//***************************************************************************************************************
-void Pintail::print(ostream& out) {
- try {
-
- for (int i = 0; i < querySeqs.size(); i++) {
-
- int index = ceil(deviation[i]);
-float quan = 2.64 * log10(deviation[i]) + 1.46;
-cout << "dist = " << index << endl;
-cout << "de = " << DE[i] << endl;
-cout << "mallard quantile = " << quan << endl;
-cout << "my quantile = " << quantiles[index][4] << endl;
-
- //is your DE value higher than the 95%
- string chimera;
- if (DE[i] > quantiles[index][4]) { chimera = "Yes"; }
- else { chimera = "No"; }
-
- out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl;
- if (chimera == "Yes") {
- mothurOut(querySeqs[i]->getName() + "\tdiv: " + toString(deviation[i]) + "\tstDev: " + toString(DE[i]) + "\tchimera flag: " + chimera); mothurOutEndLine();
- }
- out << "Observed\t";
-
- for (int j = 0; j < obsDistance[i].size(); j++) { out << obsDistance[i][j] << '\t'; }
- out << endl;
-
- out << "Expected\t";
-
- for (int m = 0; m < expectedDistance[i].size(); m++) { out << expectedDistance[i][m] << '\t'; }
- out << endl;
-
- }
- }
- catch(exception& e) {
- errorOut(e, "Pintail", "print");
- exit(1);
- }
}
-
//***************************************************************************************************************
-void Pintail::getChimeras() {
+void Pintail::doPrep() {
try {
- //read in query sequences and subject sequences
- mothurOut("Reading sequences and template file... "); cout.flush();
- querySeqs = readSeqs(fastafile);
- templateSeqs = readSeqs(templateFile);
- mothurOut("Done."); mothurOutEndLine();
-
- int numSeqs = querySeqs.size();
-
- 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);
+ mergedFilterString = "";
windowSizesTemplate.resize(templateSeqs.size(), window);
- windowsForeachQuery.resize(numSeqs);
- h.resize(numSeqs);
quantiles.resize(100); //one for every percent mismatch
+ quantilesMembers.resize(100); //one for every percent mismatch
- //break up file if needed
- int linesPerProcess = numSeqs / processors ;
+ //if the user does not enter a mask then you want to keep all the spots in the alignment
+ if (seqMask.length() == 0) { decalc->setAlignmentLength(templateSeqs[0]->getAligned().length()); }
+ else { decalc->setAlignmentLength(seqMask.length()); }
+
+ decalc->setMask(seqMask);
#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));
- }
-
//find breakup of templatefile for quantiles
if (processors == 1) { templateLines.push_back(new linePair(0, templateSeqs.size())); }
else {
}
}
#else
- lines.push_back(new linePair(0, numSeqs));
templateLines.push_back(new linePair(0, templateSeqs.size()));
#endif
-
- distcalculator = new ignoreGaps();
- decalc = new DeCalculator();
-
- //if the user does enter a mask then you want to keep all the spots in the alignment
- if (seqMask.length() == 0) { decalc->setAlignmentLength(querySeqs[0]->getAligned().length()); }
- else { decalc->setAlignmentLength(seqMask.length()); }
-
- decalc->setMask(seqMask);
-
- //find pairs
- if (processors == 1) {
- mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
- bestfit = findPairs(lines[0]->start, lines[0]->end);
- mothurOut("Done."); mothurOutEndLine();
- }else { createProcessesPairs(); }
-
-
- for (int j = 0; j < bestfit.size(); j++) {
- //chops off beginning and end of sequences so they both start and end with a base
- ofstream out;
- string s = querySeqs[j]->getName();
-
- openOutputFile(s, out);
- out << ">" << querySeqs[j]->getName() << endl;
- out << querySeqs[j]->getAligned() << endl;
- out.close();
-
- string t =querySeqs[j]->getName() + ".ref";
- openOutputFile(t, out);
- out << ">" << bestfit[j]->getName() << endl;
- out << bestfit[j]->getAligned() << endl;
- out.close();
- }
- //find P
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 frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. "); cout.flush();
- probabilityProfile = decalc->calcFreq(templateSeqs, templateFile);
+ probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName));
mothurOut("Done."); mothurOutEndLine();
- }else { probabilityProfile = readFreq(); }
-
+ }else { probabilityProfile = readFreq(); mothurOut("Done."); }
+ mothurOutEndLine();
+
//make P into Q
for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; } //cout << i << '\t' << probabilityProfile[i] << endl;
- mothurOut("Done."); mothurOutEndLine();
- //mask querys
- for (int i = 0; i < querySeqs.size(); i++) {
- //cout << querySeqs[i]->getName() << " before mask = " << querySeqs[i]->getAligned() << endl << endl;
- decalc->runMask(querySeqs[i]);
- //cout << querySeqs[i]->getName() << " after mask = " << querySeqs[i]->getAligned() << endl << endl;
- }
-
- //mask templates
- for (int i = 0; i < templateSeqs.size(); i++) {
- decalc->runMask(templateSeqs[i]);
- }
-
-//for (int i = 0; i < lines.size(); i++) { cout << "line pair " << i << " = " << lines[i]->start << '\t' << lines[i]->end << endl; }
-
- if (processors == 1) {
-
- for (int j = 0; j < bestfit.size(); j++) {
- //cout << querySeqs[j]->getName() << " after mask = " << querySeqs[j]->getAligned() << endl << endl;
- ///cout << bestfit[j]->getName() << " after mask = " << bestfit[j]->getAligned() << endl << endl;
- decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
- }
+ bool reRead = false;
+ //create filter if needed for later
+ if (filter) {
+ reRead = true;
- mothurOut("Finding window breaks... "); cout.flush();
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- it = trimmed[i].begin();
-//cout << querySeqs[i]->getName() << '\t' << "trimmed = " << it->first << '\t' << it->second << endl;
- vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
- windowsForeachQuery[i] = win;
- }
- mothurOut("Done."); mothurOutEndLine();
-
- }else { createProcessesSpots(); }
-
-
- 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 = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
-
- for (int j = 0; j < obsi.size(); j++) {
- //cout << obsi[j] << '\t';
- }
- //cout << endl;
- 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 = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
-
- Qav[i] = q;
-//cout << querySeqs[i]->getName() << endl;
-for (int j = 0; j < Qav[i].size(); j++) {
- //cout << Qav[i][j] << '\t';
-}
-//cout << endl << endl;
-
+ if (seqMask != "") {
+ //mask templates
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ decalc->runMask(templateSeqs[i]);
+ }
}
- mothurOut("Done."); mothurOutEndLine();
+ //read in all query seqs
+ ifstream in;
+ openInputFile(fastafile, in);
- mothurOut("Calculating alpha... "); cout.flush();
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- float alpha = decalc->getCoef(obsDistance[i], Qav[i]);
-//cout << querySeqs[i]->getName() << "\tcoef = " << alpha << endl;
- seqCoef[i] = alpha;
- }
- mothurOut("Done."); mothurOutEndLine();
-
-
- mothurOut("Calculating expected distance... "); cout.flush();
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- vector<float> exp = decalc->calcExpected(Qav[i], seqCoef[i]);
- expectedDistance[i] = exp;
+ vector<Sequence*> tempQuerySeqs;
+ while(!in.eof()){
+ Sequence* s = new Sequence(in);
+ gobble(in);
+
+ if (s->getName() != "") { tempQuerySeqs.push_back(s); }
}
- mothurOut("Done."); mothurOutEndLine();
+ in.close();
+ vector<Sequence*> temp;
+ //merge query seqs and template seqs
+ temp = templateSeqs;
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); }
- mothurOut("Finding deviation... "); cout.flush();
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- float de = decalc->calcDE(obsDistance[i], expectedDistance[i]);
- DE[i] = de;
-//cout << querySeqs[i]->getName() << '\t' << "de value = " << de << endl;
- it = trimmed[i].begin();
- float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
-//cout << querySeqs[i]->getName() << '\t' << "dist value = " << dist << endl;
- deviation[i] = dist;
- }
- mothurOut("Done."); mothurOutEndLine();
+ mergedFilterString = createFilter(temp, 0.5);
- }
- else { createProcesses(); }
+ //reread template seqs
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
+ }
//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 {
+ if (quanfile != "") {
+ quantiles = readQuantiles();
+ }else {
+ if ((!filter) && (seqMask != "")) { //if you didn't filter but you want to mask. if you filtered then you did mask first above.
+ reRead = true;
+ //mask templates
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ decalc->runMask(templateSeqs[i]);
+ }
+ }
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 = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
+ quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
}else { createProcessesQuan(); }
+
+ ofstream out4, out5;
+ string noOutliers, outliers;
- decalc->removeObviousOutliers(quantiles);
-
- ofstream out4;
- string o = getRootName(templateFile) + "quan";
+ if ((!filter) && (seqMask == "")) {
+ noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.quan";
+ }else if ((filter) && (seqMask == "")) {
+ noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered.quan";
+ }else if ((!filter) && (seqMask != "")) {
+ noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.masked.quan";
+ }else if ((filter) && (seqMask != "")) {
+ noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered.masked.quan";
+ }
+
+
+ decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
- openOutputFile(o, out4);
+ openOutputFile(noOutliers, out5);
//adjust quantiles
- for (int i = 0; i < quantiles.size(); i++) {
- if (quantiles[i].size() == 0) {
+ for (int i = 0; i < quantilesMembers.size(); i++) {
+ vector<float> temp;
+
+ if (quantilesMembers[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);
+ temp.push_back(0.0);
}
}else{
- sort(quantiles[i].begin(), quantiles[i].end());
+ sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers);
- vector<float> temp;
//save 10%
- temp.push_back(quantiles[i][int(quantiles[i].size() * 0.10)]);
+ temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
//save 25%
- temp.push_back(quantiles[i][int(quantiles[i].size() * 0.25)]);
+ temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
//save 50%
- temp.push_back(quantiles[i][int(quantiles[i].size() * 0.5)]);
+ temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
//save 75%
- temp.push_back(quantiles[i][int(quantiles[i].size() * 0.75)]);
+ temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
//save 95%
- temp.push_back(quantiles[i][int(quantiles[i].size() * 0.95)]);
+ temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
//save 99%
- temp.push_back(quantiles[i][int(quantiles[i].size() * 0.99)]);
+ temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
- 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;
-
+ out5 << i+1 << '\t';
+ for (int u = 0; u < temp.size(); u++) { out5 << temp[u] << '\t'; }
+ out5 << endl;
+
+ quantiles[i] = temp;
+
}
-
+
mothurOut("Done."); mothurOutEndLine();
}
-
+
+ if (reRead) {
+ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; }
+ templateSeqs.clear();
+ templateSeqs = readSeqs(templateFileName);
+ }
+
+
//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;
- delete decalc;
+ for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i]; }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Pintail", "doPrep");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+void Pintail::print(ostream& out) {
+ try {
+ int index = ceil(deviation);
+
+ //is your DE value higher than the 95%
+ string chimera;
+ if (index != 0) { //if index is 0 then its an exact match to a template seq
+ if (quantiles[index][4] == 0.0) {
+ chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
+ }else {
+ if (DE > quantiles[index][4]) { chimera = "Yes"; }
+ else { chimera = "No"; }
+ }
+ }else{ chimera = "No"; }
+
+ out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
+ if (chimera == "Yes") {
+ mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); mothurOutEndLine();
+ }
+ out << "Observed\t";
+
+ for (int j = 0; j < obsDistance.size(); j++) { out << obsDistance[j] << '\t'; }
+ out << endl;
+
+ out << "Expected\t";
+
+ for (int m = 0; m < expectedDistance.size(); m++) { out << expectedDistance[m] << '\t'; }
+ out << endl;
+
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Pintail", "print");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+int Pintail::getChimeras(Sequence* query) {
+ try {
+ querySeq = query;
+ trimmed.clear();
+ windowSizes = window;
+
+ //find pairs has to be done before a mask
+ bestfit = findPairs(query);
+
+ //if they mask
+ if (seqMask != "") {
+ decalc->runMask(query);
+ decalc->runMask(bestfit);
+ }
+
+ if (filter) { //must be done after a mask
+ runFilter(query);
+ runFilter(bestfit);
+ }
+
+
+ //trim seq
+ decalc->trimSeqs(query, bestfit, trimmed);
+
+ //find windows
+ it = trimmed.begin();
+ windowsForeachQuery = decalc->findWindows(query, it->first, it->second, windowSizes, increment);
+
+ //find observed distance
+ obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
+
+ Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
+
+ //find alpha
+ seqCoef = decalc->getCoef(obsDistance, Qav);
+
+ //calculating expected distance
+ expectedDistance = decalc->calcExpected(Qav, seqCoef);
+
+ //finding de
+ DE = decalc->calcDE(obsDistance, expectedDistance);
+
+ //find distance between query and closest match
+ it = trimmed.begin();
+ deviation = decalc->calcDist(query, bestfit, it->first, it->second);
+
+ delete bestfit;
+
+ return 0;
}
catch(exception& e) {
errorOut(e, "Pintail", "getChimeras");
}
}
-//***************************************************************************************************************
-
-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
-vector<Sequence*> Pintail::findPairs(int start, int end) {
+Sequence* Pintail::findPairs(Sequence* q) {
try {
- vector<Sequence*> seqsMatches;
-
- for(int i = start; i < end; i++){
-
- float smallest = 10000.0;
- Sequence query = *(querySeqs[i]);
- Sequence* match;
-
- for(int j = 0; j < templateSeqs.size(); j++){
-
- Sequence temp = *(templateSeqs[j]);
-
- distcalculator->calcDist(query, temp);
- float dist = distcalculator->getDist();
-
- if (dist < smallest) {
- match = templateSeqs[j];
- smallest = dist;
- }
- }
-
- seqsMatches.push_back(match);
- }
+ Sequence* seqsMatches;
+ seqsMatches = decalc->findClosest(q, templateSeqs);
return seqsMatches;
}
exit(1);
}
}
-
-/**************************************************************************************************/
-
-void Pintail::createProcessesSpots() {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
- vector<int> processIDS;
-
- //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){
-
- for (int j = lines[process]->start; j < lines[process]->end; j++) {
-
- //chops off beginning and end of sequences so they both start and end with a base
- map<int, int> trim;
- decalc->trimSeqs(querySeqs[j], bestfit[j], trim);
- trimmed[j] = trim;
-
- }
-
- 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++) {
- it = trimmed[i].begin();
- windowsForeachQuery[i] = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
- }
- mothurOut("Done finding window breaks for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
-
- //write out data to file so parent can read it
- ofstream out;
- string s = toString(getpid()) + ".temp";
- openOutputFile(s, out);
-
- //output windowsForeachQuery
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- out << windowsForeachQuery[i].size() << '\t';
- for (int j = 0; j < windowsForeachQuery[i].size(); j++) {
- out << windowsForeachQuery[i][j] << '\t';
- }
- out << endl;
- }
-
- //output windowSizes
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- out << windowSizes[i] << '\t';
- }
- out << endl;
-
- //output trimmed values
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- it = trimmed[i].begin();
-
- out << it->first << '\t' << it->second << endl;
- }
- out.close();
-
- exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
- }
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- //get data created by processes
- for (int i=0;i<processors;i++) {
- ifstream in;
- string s = toString(processIDS[i]) + ".temp";
- openInputFile(s, in);
-
- int size = lines[i]->end - lines[i]->start;
-
- int count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- int num;
- in >> num;
-
- vector<int> win; int w;
- for (int j = 0; j < num; j++) {
- in >> w;
- win.push_back(w);
- }
-
- windowsForeachQuery[count] = win;
- count++;
- gobble(in);
- }
-
- gobble(in);
- count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- int num;
- in >> num;
-
- windowSizes[count] = num;
- count++;
- }
-
- gobble(in);
-
- count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- int front, back;
- in >> front >> back;
-
- map<int, int> t;
-
- t[front] = back;
-
- trimmed[count] = t;
- count++;
-
- gobble(in);
- }
-
-
- in.close();
- remove(s.c_str());
- }
-
-
-#else
- for (int j = 0; j < bestfit.size(); j++) {
- //chops off beginning and end of sequences so they both start and end with a base
- decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
- }
-
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- it = trimmed[i].begin();
- map<int, int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
- windows[i] = win;
- }
-
-#endif
- }
- catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesSpots");
- exit(1);
- }
-}
/**************************************************************************************************/
-
-void Pintail::createProcessesPairs() {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
- vector<int> processIDS;
-
- //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){
-
- mothurOut("Finding pairs for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
- bestfit = findPairs(lines[process]->start, lines[process]->end);
- mothurOut("Done finding pairs for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
-
- //write out data to file so parent can read it
- ofstream out;
- string s = toString(getpid()) + ".temp";
- openOutputFile(s, out);
-
- //output range and size
- out << bestfit.size() << endl;
-
- //output pairs
- for (int i = 0; i < bestfit.size(); i++) {
- out << ">" << bestfit[i]->getName() << endl << bestfit[i]->getAligned() << endl;
- }
- out.close();
-
- exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
- }
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- //get data created by processes
- for (int i=0;i<processors;i++) {
- ifstream in;
- string s = toString(processIDS[i]) + ".temp";
- openInputFile(s, in);
-
- int size;
- in >> size; gobble(in);
-
- //get pairs
- int count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- Sequence* temp = new Sequence(in);
- bestfit[count] = temp;
-
- count++;
- gobble(in);
- }
-
- in.close();
- remove(s.c_str());
- }
-
-
-#else
- bestfit = findPairs(lines[0]->start, lines[0]->end);
-#endif
- }
- catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesPairs");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-void Pintail::createProcesses() {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
- vector<int> processIDS;
-
- //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){
-
- 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 = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
- obsDistance[i] = obsi;
-
- //calc Qav
- vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
-
- //get alpha
- float alpha = decalc->getCoef(obsDistance[i], q);
-
- //find expected
- vector<float> exp = decalc->calcExpected(q, alpha);
- expectedDistance[i] = exp;
-
- //get de and deviation
- float dei = decalc->calcDE(obsi, exp);
- DE[i] = dei;
-
- it = trimmed[i].begin();
- float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
- deviation[i] = dist;
- }
- mothurOut("Done calculating observed, expected and de values for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine();
-
- //write out data to file so parent can read it
- ofstream out;
- string s = toString(getpid()) + ".temp";
- openOutputFile(s, out);
-
- int size = lines[process]->end - lines[process]->start;
- out << size << endl;
-
- //output observed distances
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- out << obsDistance[i].size() << '\t';
- for (int j = 0; j < obsDistance[i].size(); j++) {
- out << obsDistance[i][j] << '\t';
- }
- out << endl;
- }
-
-
- //output expected distances
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- out << expectedDistance[i].size() << '\t';
- for (int j = 0; j < expectedDistance[i].size(); j++) {
- out << expectedDistance[i][j] << '\t';
- }
- out << endl;
- }
-
-
- //output de values
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- out << DE[i] << '\t';
- }
- out << endl;
-
- //output de values
- for (int i = lines[process]->start; i < lines[process]->end; i++) {
- out << deviation[i] << '\t';
- }
- out << endl;
-
- out.close();
-
- exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
- }
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- //get data created by processes
- for (int i=0;i<processors;i++) {
- ifstream in;
- string s = toString(processIDS[i]) + ".temp";
- openInputFile(s, in);
-
- int size;
- in >> size; gobble(in);
-
- //get observed distances
- int count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- int num;
- in >> num;
-
- vector<float> obs; float w;
- for (int j = 0; j < num; j++) {
- in >> w;
- obs.push_back(w);
- }
-
- obsDistance[count] = obs;
- count++;
- gobble(in);
- }
-
- gobble(in);
-
- //get expected distances
- count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- int num;
- in >> num;
-
- vector<float> exp; float w;
- for (int j = 0; j < num; j++) {
- in >> w;
- exp.push_back(w);
- }
-
- expectedDistance[count] = exp;
- count++;
- gobble(in);
- }
-
- gobble(in);
-
- count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- float num;
- in >> num;
-
- DE[count] = num;
- count++;
- }
-
- gobble(in);
-
- count = lines[i]->start;
- for (int m = 0; m < size; m++) {
- float num;
- in >> num;
-
- deviation[count] = num;
- count++;
- }
-
- in.close();
- remove(s.c_str());
- }
-
-
-#else
- mothurOut("Calculating observed distance... "); cout.flush();
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- vector<float> obsi = decalc->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 = decalc->findQav(windows[i], windowSizes[i], probabilityProfile, h[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 = decalc->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 = decalc->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 = decalc->calcDE(obsDistance[i], expectedDistance[i]);
- DE[i] = de;
-
- it = trimmed[i].begin();
- float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
- deviation[i] = dist;
- }
- mothurOut("Done."); mothurOutEndLine();
-
-#endif
- }
- catch(exception& e) {
- errorOut(e, "Pintail", "createProcesses");
- exit(1);
- }
-}
-
-
-/**************************************************************************************************/
-
void Pintail::createProcessesQuan() {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
process++;
}else if (pid == 0){
- quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
+ quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
//write out data to file so parent can read it
ofstream out;
//output observed distances
- for (int i = 0; i < quantiles.size(); i++) {
- out << quantiles[i].size() << '\t';
- for (int j = 0; j < quantiles[i].size(); j++) {
- out << quantiles[i][j] << '\t';
+ for (int i = 0; i < quantilesMembers.size(); i++) {
+ out << quantilesMembers[i].size() << '\t';
+ for (int j = 0; j < quantilesMembers[i].size(); j++) {
+ out << quantilesMembers[i][j].score << '\t' << quantilesMembers[i][j].member1 << '\t' << quantilesMembers[i][j].member2 << '\t';
}
out << endl;
}
int temp = processIDS[i];
wait(&temp);
}
-
+
//get data created by processes
for (int i=0;i<processors;i++) {
ifstream in;
string s = toString(processIDS[i]) + ".temp";
openInputFile(s, in);
- vector< vector<float> > quan; quan.resize(100);
+ vector< vector<quanMember> > quan;
+ quan.resize(100);
//get quantiles
for (int m = 0; m < quan.size(); m++) {
int num;
- in >> num;
-
- vector<float> q; float w;
+ in >> num;
+
+ gobble(in);
+
+ vector<quanMember> q; float w; int b, n;
for (int j = 0; j < num; j++) {
- in >> w;
- q.push_back(w);
+ in >> w >> b >> n;
+ //cout << w << '\t' << b << '\t' n << endl;
+ quanMember newMember(w, b, n);
+ q.push_back(newMember);
}
-
+//cout << "here" << endl;
quan[m] = q;
+//cout << "now here" << endl;
gobble(in);
}
-
+
//save quan in quantiles
- for (int i = 0; i < quan.size(); i++) {
+ for (int j = 0; j < quan.size(); j++) {
//put all values of q[i] into quan[i]
- quantiles[i].insert(quantiles[i].begin(), quan[i].begin(), quan[i].end());
+ for (int l = 0; l < quan[j].size(); l++) { quantilesMembers[j].push_back(quan[j][l]); }
+ //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
}
in.close();
}
#else
- quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
+ quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
#endif
}
catch(exception& e) {
projects / mothur.git / blobdiff