+++ /dev/null
-/*
- * slayer.cpp
- * Mothur
- *
- * Created by westcott on 9/25/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "slayer.h"
-
-/***********************************************************************/
-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(); }
-/***********************************************************************/
-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(query.getName(), query.getAligned());
- Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned());
- Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned());
-
- //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) {
- m->errorOut(e, "Slayer", "getResults");
- exit(1);
- }
-}
-/***********************************************************************/
-vector<data_struct> Slayer::runBellerophon(Sequence q, Sequence pA, Sequence pB, map<int, int>& spots) {
- try{
-
- vector<data_struct> data;
-
- //vertical filter
- //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 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) {
- 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;
-
- for (int i = left; i <= right; i++) {
-
- 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);
- }
- }
- }
-
- return data;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Slayer", "getSNPS");
- exit(1);
- }
-}
-/***********************************************************************/
-int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
- 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 < 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]);
- }
-
- /* 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;
- }
-
-
- //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]++; }
- }
-
- 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;
- 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);
-
- seqAligned = pA.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++; }
-
- //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++; }
-
- //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) {
- m->errorOut(e, "Slayer", "verticalFilter");
- exit(1);
- }
-}
-/***********************************************************************/
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