X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=pintail.cpp;h=7ae3ff6dbb96224197dff97db4b435880738d87b;hb=98ea55ba2d46a429f031086b4b3272780d0ec894;hp=6ccccde7f1d73154faee33a1003e13633217e0d6;hpb=348a7bac1d3c5d17ae0e4a93b78f69f4e200a190;p=mothur.git diff --git a/pintail.cpp b/pintail.cpp index 6ccccde..7ae3ff6 100644 --- a/pintail.cpp +++ b/pintail.cpp @@ -9,24 +9,23 @@ #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 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() { try { for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; } for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } + for (int i = 0; i < bestfit.size(); i++) { delete bestfit[i]; } } catch(exception& e) { errorOut(e, "Pintail", "~Pintail"); @@ -37,23 +36,36 @@ Pintail::~Pintail() { void Pintail::print(ostream& out) { try { - for (itCoef = DE.begin(); itCoef != DE.end(); itCoef++) { + mothurOutEndLine(); - out << itCoef->first->getName() << '\t' << itCoef->second << endl; + for (int i = 0; i < querySeqs.size(); i++) { + + int index = ceil(deviation[i]); + + //is your DE value higher than the 95% + string chimera; + if (quantiles[index][4] == 0.0) { + chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index); + }else { + 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"; - 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"); @@ -65,8 +77,6 @@ void Pintail::print(ostream& out) { 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); @@ -75,364 +85,396 @@ void Pintail::getChimeras() { 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)); } } - - //calculate number of iters - iters = (querySeqs[0]->getAligned().length() - window + 1) / increment; + 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); + h.resize(numSeqs); + quantiles.resize(100); //one for every percent mismatch + quantilesMembers.resize(100); //one for every percent mismatch - int linesPerProcess = processors / numSeqs; + //break up file if needed + int linesPerProcess = numSeqs / processors ; - //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)); - } + + //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 - //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(); - // itBest = bestfit.begin(); - // itBest++; itBest++; -//cout << itBest->first->getName() << '\t' << itBest->second->getName() << endl; - //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 eachGapDist(); + decalc = new DeCalculator(); - //find P - mothurOut("Calculating expected percentage differences for each sequence... "); cout.flush(); - vector probabilityProfile = calcFreq(templateSeqs); + //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()); } - //make P into Q - for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; } -//cout << "after p into Q" << endl; - //find Qav - averageProbability = findQav(probabilityProfile); -//cout << "after Qav" << endl; - //find Coefficient - maps a sequence to its coefficient - seqCoef = getCoef(averageProbability); -//cout << "after coef" << endl; - //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(); + decalc->setMask(seqMask); - //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(); + //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(); } - - //free memory - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } - delete distCalculator; +//string o = "closestmatch.eachgap.fasta"; +//ofstream out7; +//openOutputFile(o, out7); - } - catch(exception& e) { - errorOut(e, "Pintail", "getChimeras"); - exit(1); - } -} - -//*************************************************************************************************************** +//for (int i = 0; i < bestfit.size(); i++) { + //out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl; + //out7 << bestfit[i]->getAligned() << endl; +//} +//out7.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); + mothurOut("Done."); mothurOutEndLine(); + }else { probabilityProfile = readFreq(); } -vector Pintail::readSeqs(string file) { - try { - - ifstream in; - openInputFile(file, in); - vector container; + //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(); - //read in seqs and store in vector - while(!in.eof()){ - Sequence* current = new Sequence(in); + //mask sequences if the user wants to + if (seqMask != "") { + //mask querys + for (int i = 0; i < querySeqs.size(); i++) { + decalc->runMask(querySeqs[i]); + } + + //mask templates + for (int i = 0; i < templateSeqs.size(); i++) { + decalc->runMask(templateSeqs[i]); + } - if (current->getAligned() == "") { current->setAligned(current->getUnaligned()); } + for (int i = 0; i < bestfit.size(); i++) { + decalc->runMask(bestfit[i]); + } + + } + + if (filter) { + vector temp = templateSeqs; + for (int i = 0; i < querySeqs.size(); i++) { temp.push_back(querySeqs[i]); } - container.push_back(current); + createFilter(temp); - gobble(in); + runFilter(querySeqs); + runFilter(templateSeqs); + runFilter(bestfit); } - - in.close(); - return container; - - } - catch(exception& e) { - errorOut(e, "Pintail", "readSeqs"); - 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) { - try { - - for(int i = start; i < end; i++){ - - float smallest = 10000.0; - Sequence query = *(querySeqs[i]); - - for(int j = 0; j < templateSeqs.size(); j++){ - - Sequence temp = *(templateSeqs[j]); - - distCalculator->calcDist(query, temp); - float dist = distCalculator->getDist(); - - if (dist < smallest) { - - bestfit[querySeqs[i]] = templateSeqs[j]; - smallest = dist; - } + + + if (processors == 1) { + + for (int j = 0; j < bestfit.size(); j++) { + decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]); } - } + + mothurOut("Finding window breaks... "); cout.flush(); + for (int i = lines[0]->start; i < lines[0]->end; i++) { + it = trimmed[i].begin(); + vector win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment); + windowsForeachQuery[i] = win; + } + mothurOut("Done."); mothurOutEndLine(); - } - catch(exception& e) { - errorOut(e, "Pintail", "findPairs"); - exit(1); - } -} -//*************************************************************************************************************** -void Pintail::calcObserved(int start, int end) { - try { - - for(int i = start; i < end; i++){ + }else { createProcessesSpots(); } - itBest = bestfit.find(querySeqs[i]); - Sequence* query; - Sequence* subject; + if (processors == 1) { + + mothurOut("Calculating observed distance... "); cout.flush(); + for (int i = lines[0]->start; i < lines[0]->end; i++) { + vector obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]); + + obsDistance[i] = obsi; + } + mothurOut("Done."); mothurOutEndLine(); - if (itBest != bestfit.end()) { - query = itBest->first; - subject = itBest->second; - }else{ mothurOut("Error in calcObserved"); mothurOutEndLine(); } - vector queryFragment; - vector subjectFragment; + mothurOut("Finding variability... "); cout.flush(); + for (int i = lines[0]->start; i < lines[0]->end; i++) { + vector q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile); + + Qav[i] = q; + } + mothurOut("Done."); mothurOutEndLine(); + - int startpoint = 0; - for (int m = 0; m < iters; m++) { - string seqFrag = query->getAligned().substr(startpoint, window); - Sequence* temp = new Sequence(query->getName(), seqFrag); - queryFragment.push_back(temp); - - string seqFragsub = subject->getAligned().substr(startpoint, window); - Sequence* tempsub = new Sequence(subject->getName(), seqFragsub); - subjectFragment.push_back(tempsub); - - startpoint += increment; + 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[i] = alpha; + } + mothurOut("Done."); mothurOutEndLine(); + + + mothurOut("Calculating expected distance... "); cout.flush(); + for (int i = lines[0]->start; i < lines[0]->end; i++) { + vector exp = decalc->calcExpected(Qav[i], seqCoef[i]); + expectedDistance[i] = exp; } + mothurOut("Done."); mothurOutEndLine(); - for(int j = 0; j < iters; j++){ + 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; - distCalculator->calcDist(*(queryFragment[j]), *(subjectFragment[j])); - float dist = distCalculator->getDist(); - - //convert to similiarity - //dist = 1 - dist; - - //save oi - obsDistance[query].push_back(dist); + it = trimmed[i].begin(); + float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second); + deviation[i] = dist; } + mothurOut("Done."); mothurOutEndLine(); + + } + else { createProcesses(); } - //free memory - for (int i = 0; i < queryFragment.size(); i++) { delete queryFragment[i]; } - for (int i = 0; i < subjectFragment.size(); i++) { delete subjectFragment[i]; } - } - - } - catch(exception& e) { - errorOut(e, "Pintail", "calcObserved"); - exit(1); - } -} - -//*************************************************************************************************************** -void Pintail::calcExpected(int start, int end) { - try { + //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) { + quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size()); + }else { createProcessesQuan(); } - - //for each sequence - for(int i = start; i < end; i++){ - itCoef = seqCoef.find(querySeqs[i]); - float coef = itCoef->second; + ofstream out4, out5; + string noOutliers, outliers; - //for each window - vector queryExpected; - for (int m = 0; m < iters; m++) { - float expected = averageProbability[m] * coef; - queryExpected.push_back(expected); + if ((!filter) && (seqMask == "")) { + noOutliers = getRootName(templateFile) + "pintail.quan"; + }else if ((filter) && (seqMask == "")) { + noOutliers = getRootName(templateFile) + "pintail.filtered.quan"; + }else if ((!filter) && (seqMask != "")) { + noOutliers = getRootName(templateFile) + "pintail.masked.quan"; + }else if ((filter) && (seqMask != "")) { + noOutliers = getRootName(templateFile) + "pintail.filtered.masked.quan"; } + + //outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS"; - expectedDistance[querySeqs[i]] = queryExpected; + /*openOutputFile(outliers, out4); - } + //adjust quantiles + for (int i = 0; i < quantilesMembers.size(); i++) { + vector temp; - } - catch(exception& e) { - errorOut(e, "Pintail", "calcExpected"); - exit(1); - } -} -//*************************************************************************************************************** -void Pintail::calcDE(int start, int end) { - try { - - - //for each sequence - for(int i = start; i < end; i++){ + if (quantilesMembers[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(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers); + + //save 10% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score); + //save 25% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score); + //save 50% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score); + //save 75% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score); + //save 95% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score); + //save 99% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score); + + } + + //output quan value + out4 << i+1 << '\t'; + for (int u = 0; u < temp.size(); u++) { out4 << temp[u] << '\t'; } + out4 << endl; + + quantiles[i] = temp; + + } - itObsDist = obsDistance.find(querySeqs[i]); - vector obs = itObsDist->second; + out4.close();*/ - itExpDist = expectedDistance.find(querySeqs[i]); - vector exp = itExpDist->second; + decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size()); - //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])); } + openOutputFile(noOutliers, out5); - float de = sqrt((sum / (iters - 1))); + //adjust quantiles + for (int i = 0; i < quantilesMembers.size(); i++) { + vector 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++) { + temp.push_back(0.0); + } + }else{ + + sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers); + + //save 10% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score); + //save 25% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score); + //save 50% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score); + //save 75% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score); + //save 95% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score); + //save 99% + temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score); + + } + + //output quan value + out5 << i+1 << '\t'; + for (int u = 0; u < temp.size(); u++) { out5 << temp[u] << '\t'; } + out5 << endl; + + quantiles[i] = temp; + + } + + mothurOut("Done."); mothurOutEndLine(); - DE[querySeqs[i]] = de; } - + + //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; } catch(exception& e) { - errorOut(e, "Pintail", "calcDE"); + errorOut(e, "Pintail", "getChimeras"); exit(1); } } //*************************************************************************************************************** -vector Pintail::calcFreq(vector seqs) { +vector Pintail::readFreq() { try { - + + ifstream in; + openInputFile(consfile, in); + vector prob; + set h = decalc->getPos(); //positions of bases in masking sequence - //at each position in the sequence - for (int i = 0; i < seqs[0]->getAligned().length(); i++) { + //read in probabilities and store in vector + int pos; float num; - vector freq; freq.resize(4,0); + while(!in.eof()){ - //find the frequency of each nucleotide - for (int j = 0; j < seqs.size(); j++) { - - char value = seqs[j]->getAligned()[i]; + in >> pos >> num; - 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]++; } - } + if (h.count(pos) > 0) { + float Pi; + Pi = (num - 0.25) / 0.75; - //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; - //if this is not a gap column - if (highFreq != 0) { Pi = (highFreq - 0.25) / 0.75; } - else { Pi = 0; } - - prob.push_back(Pi); + //cannot have probability less than 0. + if (Pi < 0) { Pi = 0.0; } + + //do you want this spot + prob.push_back(Pi); + } + gobble(in); } + in.close(); return prob; - - } - catch(exception& e) { - errorOut(e, "Pintail", "calcFreq"); - exit(1); - } -} -//*************************************************************************************************************** -vector Pintail::findQav(vector prob) { - try { - vector averages; - - //for each window find average - int startpoint = 0; - for (int m = 0; m < iters; m++) { - - float average = 0.0; - for (int i = startpoint; i < (startpoint+window); i++) { average += prob[i]; } - - average = average / window; - - //save this windows average - averages.push_back(average); - - startpoint += increment; - } - return averages; } catch(exception& e) { - errorOut(e, "Pintail", "findQav"); + errorOut(e, "Pintail", "readFreq"); exit(1); } } + //*************************************************************************************************************** -map Pintail::getCoef(vector prob) { +//calculate the distances from each query sequence to all sequences in the template to find the closest sequence +vector Pintail::findPairs(int start, int end) { try { - map coefs; - //find average prob - float probAverage = 0.0; - for (int i = 0; i < prob.size(); i++) { probAverage += prob[i]; } - probAverage = probAverage / (float) prob.size(); + vector seqsMatches; - //find a coef for each sequence - map >::iterator it; - for (it = obsDistance.begin(); it != obsDistance.end(); it++) { - - vector temp = it->second; - Sequence* tempSeq = it->first; + for(int i = start; i < end; i++){ + + float smallest = 10000.0; + Sequence query = *(querySeqs[i]); + Sequence* match; - //find observed average - float obsAverage = 0.0; - for (int i = 0; i < temp.size(); i++) { obsAverage += temp[i]; } - obsAverage = obsAverage / (float) temp.size(); + 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; + } + } - float coef = obsAverage / probAverage; + //make copy so trimSeqs doesn't overtrim + Sequence* copy = new Sequence(match->getName(), match->getAligned()); - //save this sequences coefficient - coefs[tempSeq] = coef; + seqsMatches.push_back(copy); } - - return coefs; + return seqsMatches; + } catch(exception& e) { - errorOut(e, "Pintail", "getCoef"); + errorOut(e, "Pintail", "findPairs"); exit(1); } } /**************************************************************************************************/ -void Pintail::createProcessesPairs() { +void Pintail::createProcessesSpots() { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; @@ -446,7 +488,51 @@ void Pintail::createProcessesPairs() { processIDS.push_back(pid); process++; }else if (pid == 0){ - findPairs(lines[process]->start, lines[process]->end); + + 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 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); } } @@ -457,20 +543,85 @@ void Pintail::createProcessesPairs() { wait(&temp); } + //get data created by processes + for (int i=0;iend - lines[i]->start; + + int count = lines[i]->start; + for (int m = 0; m < size; m++) { + int num; + in >> num; + + vector 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 t; + + t[front] = back; + + trimmed[count] = t; + count++; + + gobble(in); + } + + + in.close(); + remove(s.c_str()); + } + + #else - 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 + decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]); + } + + for (int i = lines[0]->start; i < lines[0]->end; i++) { + it = trimmed[i].begin(); + vector win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment); + windowsForeachQuery[i] = win; + } #endif } catch(exception& e) { - errorOut(e, "Pintail", "createProcessesPairs"); + errorOut(e, "Pintail", "createProcessesSpots"); exit(1); } } - /**************************************************************************************************/ -void Pintail::createProcessesObserved() { +void Pintail::createProcessesPairs() { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; @@ -484,7 +635,25 @@ void Pintail::createProcessesObserved() { 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(); + 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); } } @@ -495,20 +664,42 @@ void Pintail::createProcessesObserved() { wait(&temp); } + //get data created by processes + for (int i=0;i> 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 - calcObserved(lines[0]->start, lines[0]->end); - + bestfit = findPairs(lines[0]->start, lines[0]->end); #endif } catch(exception& e) { - errorOut(e, "Pintail", "createProcessesObserved"); + errorOut(e, "Pintail", "createProcessesPairs"); exit(1); } } +/**************************************************************************************************/ -//*************************************************************************************************************** - -void Pintail::createProcessesExpected() { +void Pintail::createProcesses() { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; @@ -522,7 +713,75 @@ void Pintail::createProcessesExpected() { 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 obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]); + obsDistance[i] = obsi; + + //calc Qav + vector q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile); + + //get alpha + float alpha = decalc->getCoef(obsDistance[i], q); + + //find expected + vector 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); } } @@ -533,25 +792,143 @@ void Pintail::createProcessesExpected() { wait(&temp); } + //get data created by processes + for (int i=0;i> size; gobble(in); + + //get observed distances + int count = lines[i]->start; + for (int m = 0; m < size; m++) { + int num; + in >> num; + + vector 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 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 - 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 obsi = decalc->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 q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile); + 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 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", "createProcessesExpected"); + errorOut(e, "Pintail", "createProcesses"); exit(1); } } + /**************************************************************************************************/ -void Pintail::createProcessesDE() { +void Pintail::createProcessesQuan() { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; vector processIDS; - + //loop through and create all the processes you want while (process != processors) { int pid = fork(); @@ -560,7 +937,26 @@ void Pintail::createProcessesDE() { processIDS.push_back(pid); process++; }else if (pid == 0){ - calcDE(lines[process]->start, lines[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; + string s = toString(getpid()) + ".temp"; + openOutputFile(s, out); + + + //output observed distances + 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; + } + + out.close(); + exit(0); }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); } } @@ -570,18 +966,59 @@ void Pintail::createProcessesDE() { int temp = processIDS[i]; wait(&temp); } + + //get data created by processes + for (int i=0;i > quan; + quan.resize(100); + + //get quantiles + for (int m = 0; m < quan.size(); m++) { + int num; + in >> num; + + gobble(in); + + vector q; float w; int b, n; + for (int j = 0; j < num; j++) { + 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 j = 0; j < quan.size(); j++) { + //put all values of q[i] into quan[i] + 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(); + remove(s.c_str()); + } #else - calcDE(lines[0]->start, lines[0]->end); - + quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size()); #endif } catch(exception& e) { - errorOut(e, "Pintail", "createProcessesDE"); + errorOut(e, "Pintail", "createProcessesQuan"); exit(1); } } + //***************************************************************************************************************