#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<Sequence*> refSeqs) {
+string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
try {
+ vector<data_struct> 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());
- vector<data_struct> divs = runBellerophon(q, leftParent, rightParent);
+ map<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
+ vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
+
+ if (m->control_pressed) {
+ delete q;
+ delete leftParent;
+ delete rightParent;
+ return "no";
+ }
+
+ vector<data_struct> selectedDivs;
+ for (int k = 0; k < divs.size(); k++) {
+
+ vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
+ vector<snps> 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]);
+ //}
+ }
+ }
+
+ //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<data_struct> Slayer::runBellerophon(Sequence* query, Sequence* parentA, Sequence* parentB) {
+vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
try{
vector<data_struct> data;
//vertical filter
vector<Sequence*> 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;
+ }
- int alignLength = query->getAligned().length();
+ 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);
+
+ 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) {
+ m->errorOut(e, "Slayer", "runBellerophon");
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
+ try {
+
+ vector<snps> 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) {
- errorOut(e, "Slayer", "runBellerophon");
+ m->errorOut(e, "Slayer", "getSNPS");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> 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<snps> selectedLeft;
+
+ for (int j = 0; j < numLeft; j++) {
+ int index = int(rand() % left.size());
+ selectedLeft.push_back(left[index]);
+ }
+
+ vector<snps> 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<snps> 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<snps> 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<snps> 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);
}
}
try {
int total = 0;
int matches = 0;
-
+
for (int i = left; i <= right; i++) {
total++;
if (queryFrag[i] == parent[i]) {
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<Sequence*> seqs) {
+//remove columns that contain any gaps
+map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
try {
+ //find baseSpots
+ baseSpots.clear();
+ baseSpots.resize(3); //query, parentA, parentB
+
vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
string filterString = (string(seqs[0]->getAligned().length(), '1'));
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<int, int> 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);
}
}
projects / mothur.git / blobdiff