#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, int mi) :
+ minBS(mi), 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();
+ myQuery = query;
+
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());
+ Sequence q(query.getName(), query.getAligned());
+ Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned());
+ Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned());
- vector<data_struct> divs = runBellerophon(q, leftParent, rightParent);
-
- delete q;
- delete leftParent;
- delete rightParent;
+ //cout << q->getName() << endl << q->getAligned() << endl << endl;
+ //cout << leftParent.getName() << '\t' << leftParent.getAligned().length() << endl << endl;
+ //cout << rightParent.getName() << '\t' << rightParent.getAligned().length() << endl << endl;
+ //cout << q.getName() << '\t' << q.getAligned().length() << endl << endl;
+ //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;
+ //cout << " length = " << rightParent->getAligned().length() << endl;
+
+ 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) { return "no"; }
+// cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl;
+ 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) { return "no"; }
+
+ int numSNPSLeft = snpsLeft.size();
+ int numSNPSRight = snpsRight.size();
+
+// cout << numSNPSLeft << '\t' << numSNPSRight << endl;
+ //require at least 4 SNPs on each side of the break
+ if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
+
+ float BS_A, BS_B;
+ bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
+
+ if (m->control_pressed) { 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);
+
+
+ //are we within 10 points of the bootstrap cutoff?
+// if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
+// bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
+//
+// 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 mi = 0; mi < selectedDivs.size(); mi++) { all.push_back(selectedDivs[mi]); }
}
-
}
-
+
+ // 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);
+ //cout << q.getName() << endl << q.getAligned() << endl << endl;
+ //cout << pA.getName() << endl << pA.getUnaligned() << endl << endl;
+ //cout << pB.getName() << endl << pB.getUnaligned() << endl << endl;
+
+ //maps spot in new alignment to spot in alignment before filter
+ spots = verticalFilter(q, pA, pB); //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.getUnaligned() << endl << endl;
+//cout << pB.getName() << endl << pB.getUnaligned() << endl << endl;
+//cout << " length = " << length << 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 alignLength = query->getAligned().length();
+ 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 << q->getName() << '\t';
+ //cout << pA->getName() << '\t';
+ //cout << pB->getName() << '\t';
+ //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
+ //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
+//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);
}
}
/***********************************************************************/
-float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
+vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
try {
- int total = 0;
- int matches = 0;
+ vector<snps> data;
+
for (int i = left; i <= right; i++) {
- total++;
- if (queryFrag[i] == parent[i]) {
- matches++;
+
+ char A = parentA[i];
+ char Q = query[i];
+ char B = parentB[i];
+
+ if ((A != Q) || (B != Q)) {
+
+ //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()-1 || 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()-1 || 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()-1 || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
+ )
+ {
+ snps member;
+ member.queryChar = Q;
+ member.parentAChar = A;
+ member.parentBChar = B;
+ data.push_back(member);
+ }
}
}
-
- float percentID =( matches/(float)total) * 100;
- return percentID;
+ return data;
+
}
catch(exception& e) {
- errorOut(e, "Slayer", "computePercentID");
+ m->errorOut(e, "Slayer", "getSNPS");
exit(1);
}
}
/***********************************************************************/
-//this is a vertical filter
-void Slayer::verticalFilter(vector<Sequence*> seqs) {
+int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
try {
- vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
+
+ 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 < numIters; 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]);
+ }
- string filterString = (string(seqs[0]->getAligned().length(), '1'));
+ /* A ------------------------------------------
+ # QLA QRA
+ # Q ------------------------------------------
+ # |
+ # |
+ # Q ------------------------------------------
+ # QLB QRB
+ # B ------------------------------------------ */
- //for each sequence
- for (int i = 0; i < seqs.size(); i++) {
- string seqAligned = seqs[i]->getAligned();
+ 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++;
+ }
- for (int j = 0; j < seqAligned.length(); j++) {
- //if this spot is a gap
- if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; }
+//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;
+ }
+
+
+ //cout << count_A << '\t' << count_B << endl;
+
+ BSA = (float) count_A / (float) numIters * 100;
+ BSB = (float) count_B / (float) numIters * 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);
+ }
+}
+/***********************************************************************/
+float Slayer::computePercentID(string queryAlign, string chimera, int left, int right) {
+ try {
+
+ int numIdentical = 0;
+ int countA = 0;
+ int countB = 0;
+ for (int i = left; i <= right; i++) {
+ if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
+ ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
+ else {
+
+ bool charA = false; bool charB = false;
+ if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
+ if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
+
+ if (charA || charB) {
+
+ if (charA) { countA++; }
+ if (charB) { countB++; }
+
+ if (queryAlign[i] == chimera[i]) {
+ numIdentical++;
+ }
+ }
}
+
+ }
+
+ float numBases = (countA + countB) /(float) 2;
+
+ if (numBases == 0) { return 0; }
+
+ float percentIdentical = (numIdentical/(float)numBases) * 100;
+
+ return percentIdentical;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Slayer", "computePercentID");
+ exit(1);
+ }
+}
+/***********************************************************************/
+//remove columns that contain any gaps
+map<int, int> Slayer::verticalFilter(Sequence& q, Sequence& pA, Sequence& pB) {
+ try {
+ //find baseSpots
+ baseSpots.clear();
+ baseSpots.resize(3); //query, parentA, parentB
+
+ vector<int> gaps; gaps.resize(q.getAligned().length(), 0);
+
+ string filterString = (string(q.getAligned().length(), '1'));
+
+ string seqAligned = q.getAligned();
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is a gap
+ if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; }
+ }
+
+ seqAligned = pA.getAligned();
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is a gap
+ if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; }
}
- //zero out spot where all sequences have blanks
+ seqAligned = pB.getAligned();
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is a gap
+ if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; }
+ }
+
+
+ //zero out spot where any sequences have blanks
int numColRemoved = 0;
- for(int i = 0; i < seqs[0]->getAligned().length(); i++){
- if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
+ int count = 0;
+ map<int, int> maskMap; maskMap.clear();
+
+ for(int i = 0; i < q.getAligned().length(); i++){
+ if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; }
+ else {
+ maskMap[count] = i;
+ count++;
+ }
+ }
+
+ seqAligned = q.getAligned();
+ string newAligned = "";
+
+ int baseCount = 0;
+ 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];
+ baseSpots[0][count] = baseCount;
+ count++;
+ }
}
+
+ q.setAligned(newAligned);
- //for each sequence
- for (int i = 0; i < seqs.size(); i++) {
+ seqAligned = pA.getAligned();
+ newAligned = "";
- string seqAligned = seqs[i]->getAligned();
- string newAligned = "";
+ baseCount = 0;
+ count = 0;
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //are you a base
+ if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; }
- for (int j = 0; j < seqAligned.length(); j++) {
- //if this spot is not a gap
- if (filterString[j] == '1') { newAligned += seqAligned[j]; }
+ //if this spot is not a gap
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ baseSpots[1][count] = baseCount;
+ count++;
}
+ }
+
+ pA.setAligned(newAligned);
+
+ seqAligned = pB.getAligned();
+ newAligned = "";
+
+ baseCount = 0;
+ count = 0;
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //are you a base
+ if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; }
- seqs[i]->setAligned(newAligned);
+ //if this spot is not a gap
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ baseSpots[2][count] = baseCount;
+ count++;
+ }
}
+
+ pB.setAligned(newAligned);
+
+
+ return maskMap;
}
catch(exception& e) {
- errorOut(e, "Slayer", "verticalFilter");
+ m->errorOut(e, "Slayer", "verticalFilter");
exit(1);
}
}
projects / mothur.git / blobdiff