X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.cpp;h=1c9039087419572d1cd7fca638ab68e752894c67;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=d838a2e86857bbce9a3375b795abe17964cbeaf0;hpb=05a0195e07c42c996592ee1c8abb63adedb7f493;p=mothur.git diff --git a/slayer.cpp b/slayer.cpp index d838a2e..1c90390 100644 --- a/slayer.cpp +++ b/slayer.cpp @@ -10,57 +10,431 @@ #include "slayer.h" /***********************************************************************/ -Slayer::Slayer(int win, int increment, int parentThreshold, float div) : - windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div) {} +Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp) : + windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); } /***********************************************************************/ -void Slayer::getResults(Sequence* query, vector refSeqs) { +string Slayer::getResults(Sequence* query, vector refSeqs) { try { + vector all; all.clear(); for (int i = 0; i < refSeqs.size(); i++) { for (int j = i+1; j < refSeqs.size(); j++) { + if (m->control_pressed) { return "no"; } + //make copies of query and each parent because runBellerophon removes gaps and messes them up Sequence* q = new Sequence(query->getName(), query->getAligned()); Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned()); Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned()); + + map spots; //map from spot in original sequence to spot in filtered sequence for query and both parents + vector divs = runBellerophon(q, leftParent, rightParent, spots); + + if (m->control_pressed) { + delete q; + delete leftParent; + delete rightParent; + return "no"; + } + + vector selectedDivs; + for (int k = 0; k < divs.size(); k++) { + + vector snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd); + vector snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd); + + if (m->control_pressed) { + delete q; + delete leftParent; + delete rightParent; + return "no"; + } + + int numSNPSLeft = snpsLeft.size(); + int numSNPSRight = snpsRight.size(); + + //require at least 3 SNPs on each side of the break + if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) { + + //removed in 12/09 version of chimeraSlayer + //int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1; + //int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1; + + //float snpRateLeft = numSNPSLeft / (float) winSizeLeft; + //float snpRateRight = numSNPSRight / (float) winSizeRight; + //float logR = log(snpRateLeft / snpRateRight) / log(2.0); + + // do not accept excess snp ratio on either side of the break + //if (abs(logR) < 1 ) { + + float BS_A, BS_B; + bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B); + + if (m->control_pressed) { + delete q; + delete leftParent; + delete rightParent; + return "no"; + } + + divs[k].bsa = BS_A; + divs[k].bsb = BS_B; + + divs[k].bsMax = max(BS_A, BS_B); + + divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra); + + //so results reflect orignal alignment + divs[k].winLStart = spots[divs[k].winLStart]; + divs[k].winLEnd = spots[divs[k].winLEnd]; + divs[k].winRStart = spots[divs[k].winRStart]; + divs[k].winREnd = spots[divs[k].winREnd]; + + selectedDivs.push_back(divs[k]); + //} + } + } - vector divs = runBellerophon(q, leftParent, rightParent); + //save selected + for (int m = 0; m < selectedDivs.size(); m++) { all.push_back(selectedDivs[m]); } delete q; delete leftParent; delete rightParent; } - } - + // compute bootstrap support + if (all.size() > 0) { + //sort them + sort(all.begin(), all.end(), compareDataStruct); + reverse(all.begin(), all.end()); + + outputResults = all; + return "yes"; + } + else { + outputResults = all; + return "no"; + } } catch(exception& e) { - errorOut(e, "Slayer", "getResults"); + m->errorOut(e, "Slayer", "getResults"); exit(1); } } /***********************************************************************/ -vector Slayer::runBellerophon(Sequence* query, Sequence* parentA, Sequence* parentB) { +vector Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map& spots) { try{ vector data; //vertical filter vector temp; - verticalFilter(temp); + temp.push_back(q); temp.push_back(pA); temp.push_back(pB); + + //maps spot in new alignment to spot in alignment before filter + spots = verticalFilter(temp); //fills baseSpots + + //get these to avoid numerous function calls + string query = q->getAligned(); + string parentA = pA->getAligned(); + string parentB = pB->getAligned(); + int length = query.length(); +/*cout << q->getName() << endl << q->getAligned() << endl << endl; +cout << pA->getName() << endl << pA->getAligned() << endl << endl; +cout << pB->getName() << endl << pB->getAligned() << endl << endl; +cout << " length = " << length << endl; +cout << q->getName() << endl; +cout << pA->getName() << '\t'; +cout << pB->getName() << endl;*/ + + //check window size + if (length < (2*windowSize+windowStep)) { +// m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine(); + windowSize = length / 4; + } + + for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) { + + if (m->control_pressed) { return data; } + + int breakpoint = i; + int leftLength = breakpoint + 1; + int rightLength = length - leftLength; + + float QLA = computePercentID(query, parentA, 0, breakpoint); + float QRB = computePercentID(query, parentB, breakpoint+1, length - 1); + + float QLB = computePercentID(query, parentB, 0, breakpoint); + float QRA = computePercentID(query, parentA, breakpoint+1, length - 1); - int alignLength = query->getAligned().length(); + float LAB = computePercentID(parentA, parentB, 0, breakpoint); + float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1); + float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length; + float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length; + float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length; + float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length; + float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length; + //in original and not used + //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length; + + float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB)); + float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB)); +//cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' << QLB_QRA << endl; + +//cout << divRThreshold << endl; +//cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl; + //is one of them above the + if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) { + + if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold)) || + ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold))) { + + data_struct member; + + member.divr_qla_qrb = divR_QLA_QRB; + member.divr_qlb_qra = divR_QLB_QRA; + member.qla_qrb = QLA_QRB; + member.qlb_qra = QLB_QRA; + member.qla = QLA; + member.qrb = QRB; + member.ab = AB; + member.qa = QA; + member.qb = QB; + member.lab = LAB; + member.rab = RAB; + member.qra = QRA; + member.qlb = QLB; + member.winLStart = 0; + member.winLEnd = breakpoint; + member.winRStart = breakpoint+1; + member.winREnd = length-1; + member.querySeq = *(q); + member.parentA = *(pA); + member.parentB = *(pB); + member.bsa = 0; + member.bsb = 0; + member.bsMax = 0; + member.chimeraMax = 0; + + data.push_back(member); + + }//if + }//if + }//for return data; } catch(exception& e) { - errorOut(e, "Slayer", "runBellerophon"); + m->errorOut(e, "Slayer", "runBellerophon"); + exit(1); + } +} +/***********************************************************************/ +vector Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) { + try { + + vector data; +//cout << left << '\t' << right << endl; + for (int i = left; i <= right; i++) { + + char A = parentA[i]; + char Q = query[i]; + char B = parentB[i]; + + if ((A != Q) || (B != Q)) { +//cout << "not equal " << Q << '\t' << A << '\t' << B << endl; + + //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS + if ( + //did query loose a base here during filter?? + ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) && + ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1) + && + //did parentA loose a base here during filter?? + ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) && + ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1) + && + //did parentB loose a base here during filter?? + ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) && + ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1) + ) + { + + snps member; + member.queryChar = Q; + member.parentAChar = A; + member.parentBChar = B; +//cout << "not neighboring a gap " << Q << '\t' << A << '\t' << B << '\t' << baseSpots[0][i] << '\t' << baseSpots[0][i+1] << '\t' << baseSpots[0][i-1] << '\t' << baseSpots[1][i] << '\t' << baseSpots[1][i+1] << '\t' << baseSpots[1][i-1] << '\t' << baseSpots[2][i] << '\t' << baseSpots[2][i+1] << '\t' << baseSpots[2][i-1] << endl; + data.push_back(member); + } + } + } + + return data; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "getSNPS"); + exit(1); + } +} +/***********************************************************************/ +int Slayer::bootstrapSNPS(vector left, vector right, float& BSA, float& BSB) { + try { + + srand((unsigned)time( NULL )); + + int count_A = 0; // sceneario QLA,QRB supported + int count_B = 0; // sceneario QLB,QRA supported + + int numLeft = max(1, int(left.size() * (percentSNPSample/(float)100) + 0.5)); + int numRight = max(1, int(right.size() * (percentSNPSample/(float)100) + 0.5)); + + for (int i = 0; i < iters; i++) { + //random sampling with replacement. + + if (m->control_pressed) { return 0; } + + vector selectedLeft; + + for (int j = 0; j < numLeft; j++) { + int index = int(rand() % left.size()); + selectedLeft.push_back(left[index]); + } + + vector selectedRight; + for (int j = 0; j < numRight; j++) { + int index = int(rand() % right.size()); + selectedRight.push_back(right[index]); + } + + /* A ------------------------------------------ + # QLA QRA + # Q ------------------------------------------ + # | + # | + # Q ------------------------------------------ + # QLB QRB + # B ------------------------------------------ */ + + + float QLA = snpQA(selectedLeft); + float QRA = snpQA(selectedRight); + + float QLB = snpQB(selectedLeft); + float QRB = snpQB(selectedRight); + + //in original - not used - not sure why? + //float ALB = snpAB(selectedLeft); + //float ARB = snpAB(selectedRight); + + if ((QLA > QLB) && (QRB > QRA)) { + count_A++; + } + + if ((QLB > QLA) && (QRA > QRB)) { + count_B++; + } + +//cout << "selected left snp: \n"; +//for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].parentAChar; } +//cout << endl; +//for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].queryChar; } +//cout << endl; +//for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].parentBChar; } +//cout << endl; +//cout << "selected right snp: \n"; +//for (int j = 0; j < selectedRight.size(); j++) { cout << selectedRight[j].parentAChar; } +//cout << endl; +//for (int i = 0; i < selectedRight.size(); i++) { cout << selectedRight[i].queryChar; } +//cout << endl; +//for (int i = 0; i < selectedRight.size(); i++) { cout << selectedRight[i].parentBChar; } +//cout << endl; + } + + + + + BSA = ((float) count_A / (float) iters) * 100; + BSB = ((float) count_B / (float) iters) * 100; +//cout << "bsa = " << BSA << " bsb = " << BSB << endl; + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "bootstrapSNPS"); + exit(1); + } +} +/***********************************************************************/ +float Slayer::snpQA(vector data) { + try { + + int numIdentical = 0; + + for (int i = 0; i < data.size(); i++) { + if (data[i].parentAChar == data[i].queryChar) { + numIdentical++; + } + } + + float percentID = (numIdentical / (float) data.size()) * 100; + + return percentID; + } + catch(exception& e) { + m->errorOut(e, "Slayer", "snpQA"); + exit(1); + } +} +/***********************************************************************/ +float Slayer::snpQB(vector data) { + try { + + int numIdentical = 0; + + for (int i = 0; i < data.size(); i++) { + if (data[i].parentBChar == data[i].queryChar) { + numIdentical++; + } + } + + float percentID = (numIdentical / (float) data.size()) * 100; + + return percentID; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "snpQB"); + exit(1); + } +} +/***********************************************************************/ +float Slayer::snpAB(vector data) { + try { + int numIdentical = 0; + + for (int i = 0; i < data.size(); i++) { + if (data[i].parentAChar == data[i].parentBChar) { + numIdentical++; + } + } + + float percentID = (numIdentical / (float) data.size()) * 100; + + return percentID; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "snpAB"); exit(1); } } @@ -69,7 +443,7 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri try { int total = 0; int matches = 0; - + for (int i = left; i <= right; i++) { total++; if (queryFrag[i] == parent[i]) { @@ -82,14 +456,18 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri return percentID; } catch(exception& e) { - errorOut(e, "Slayer", "computePercentID"); + m->errorOut(e, "Slayer", "computePercentID"); exit(1); } } /***********************************************************************/ -//this is a vertical filter -void Slayer::verticalFilter(vector seqs) { +//remove columns that contain any gaps +map Slayer::verticalFilter(vector seqs) { try { + //find baseSpots + baseSpots.clear(); + baseSpots.resize(3); //query, parentA, parentB + vector gaps; gaps.resize(seqs[0]->getAligned().length(), 0); string filterString = (string(seqs[0]->getAligned().length(), '1')); @@ -101,32 +479,50 @@ void Slayer::verticalFilter(vector seqs) { for (int j = 0; j < seqAligned.length(); j++) { //if this spot is a gap - if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; } + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } } } - //zero out spot where all sequences have blanks + //zero out spot where any sequences have blanks int numColRemoved = 0; + int count = 0; + map maskMap; maskMap.clear(); + for(int i = 0; i < seqs[0]->getAligned().length(); i++){ - if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; } + if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; } + else { + maskMap[count] = i; + count++; + } } - + //for each sequence for (int i = 0; i < seqs.size(); i++) { string seqAligned = seqs[i]->getAligned(); string newAligned = ""; + int baseCount = 0; + int count = 0; for (int j = 0; j < seqAligned.length(); j++) { + //are you a base + if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } + //if this spot is not a gap - if (filterString[j] == '1') { newAligned += seqAligned[j]; } + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[i][count] = baseCount; + count++; + } } seqs[i]->setAligned(newAligned); } + + return maskMap; } catch(exception& e) { - errorOut(e, "Slayer", "verticalFilter"); + m->errorOut(e, "Slayer", "verticalFilter"); exit(1); } }