5 * Created by westcott on 9/25/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
12 /***********************************************************************/
13 Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) :
14 minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
15 /***********************************************************************/
16 string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
18 vector<data_struct> all; all.clear();
21 for (int i = 0; i < refSeqs.size(); i++) {
23 for (int j = i+1; j < refSeqs.size(); j++) {
25 if (m->control_pressed) { return "no"; }
27 //make copies of query and each parent because runBellerophon removes gaps and messes them up
28 Sequence* q = new Sequence(query->getName(), query->getAligned());
29 Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
30 Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
32 //cout << q->getName() << endl << q->getAligned() << endl << endl;
33 //cout << leftParent->getName() << endl << leftParent->getAligned() << endl << endl;
34 //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;
35 //cout << " length = " << rightParent->getAligned().length() << endl;
37 map<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
38 vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
40 if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
41 // cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl;
42 vector<data_struct> selectedDivs;
43 for (int k = 0; k < divs.size(); k++) {
45 vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
46 vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
48 if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
50 int numSNPSLeft = snpsLeft.size();
51 int numSNPSRight = snpsRight.size();
53 // cout << numSNPSLeft << '\t' << numSNPSRight << endl;
54 //require at least 4 SNPs on each side of the break
55 if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
58 bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
60 if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
64 divs[k].bsMax = max(BS_A, BS_B);
65 divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
68 //are we within 10 points of the bootstrap cutoff?
69 // if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
70 // bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
72 // if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
74 // divs[k].bsa = BS_A;
75 // divs[k].bsb = BS_B;
76 // divs[k].bsMax = max(BS_A, BS_B);
77 // divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
80 //so results reflect orignal alignment
81 divs[k].winLStart = spots[divs[k].winLStart];
82 divs[k].winLEnd = spots[divs[k].winLEnd];
83 divs[k].winRStart = spots[divs[k].winRStart];
84 divs[k].winREnd = spots[divs[k].winREnd];
86 selectedDivs.push_back(divs[k]);
91 for (int mi = 0; mi < selectedDivs.size(); mi++) { all.push_back(selectedDivs[mi]); }
100 // compute bootstrap support
101 if (all.size() > 0) {
103 sort(all.begin(), all.end(), compareDataStruct);
104 reverse(all.begin(), all.end());
113 catch(exception& e) {
114 m->errorOut(e, "Slayer", "getResults");
118 /***********************************************************************/
119 vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map<int, int>& spots) {
122 vector<data_struct> data;
125 vector<Sequence*> temp;
126 temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
128 //maps spot in new alignment to spot in alignment before filter
129 spots = verticalFilter(temp); //fills baseSpots
131 //get these to avoid numerous function calls
132 string query = q->getAligned();
133 string parentA = pA->getAligned();
134 string parentB = pB->getAligned();
135 int length = query.length();
136 //cout << q->getName() << endl << q->getAligned() << endl << endl;
137 //cout << pA->getName() << endl << pA->getUnaligned() << endl << endl;
138 //cout << pB->getName() << endl << pB->getUnaligned() << endl << endl;
139 //cout << " length = " << length << endl;
142 if (length < (2*windowSize+windowStep)) {
143 // 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();
144 windowSize = length / 4;
147 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
149 if (m->control_pressed) { return data; }
152 int leftLength = breakpoint + 1;
153 int rightLength = length - leftLength;
155 float QLA = computePercentID(query, parentA, 0, breakpoint);
156 float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
158 float QLB = computePercentID(query, parentB, 0, breakpoint);
159 float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
161 float LAB = computePercentID(parentA, parentB, 0, breakpoint);
162 float RAB = computePercentID(parentA, parentB, breakpoint+1, length-1);
164 float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
165 float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
166 float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
168 float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
169 float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
171 //in original and not used
172 //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
174 float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
175 float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
178 //cout << q->getName() << '\t';
179 //cout << pA->getName() << '\t';
180 //cout << pB->getName() << '\t';
181 //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
182 //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
183 //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;
185 //cout << divRThreshold << endl;
186 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
187 //is one of them above the
188 if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
190 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold)) ||
191 ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold))) {
195 member.divr_qla_qrb = divR_QLA_QRB;
196 member.divr_qlb_qra = divR_QLB_QRA;
197 member.qla_qrb = QLA_QRB;
198 member.qlb_qra = QLB_QRA;
208 member.winLStart = 0;
209 member.winLEnd = breakpoint;
210 member.winRStart = breakpoint+1;
211 member.winREnd = length-1;
212 member.querySeq = *(q);
213 member.parentA = *(pA);
214 member.parentB = *(pB);
218 member.chimeraMax = 0;
220 data.push_back(member);
230 catch(exception& e) {
231 m->errorOut(e, "Slayer", "runBellerophon");
235 /***********************************************************************/
236 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
241 for (int i = left; i <= right; i++) {
247 if ((A != Q) || (B != Q)) {
249 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
253 //did query loose a base here during filter??
254 ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
255 ( i == query.length()-1 || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
257 //did parentA loose a base here during filter??
258 ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
259 ( i == parentA.length()-1 || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
261 //did parentB loose a base here during filter??
262 ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
263 ( i == parentB.length()-1 || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
267 member.queryChar = Q;
268 member.parentAChar = A;
269 member.parentBChar = B;
270 data.push_back(member);
278 catch(exception& e) {
279 m->errorOut(e, "Slayer", "getSNPS");
283 /***********************************************************************/
284 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
287 srand((unsigned)time( NULL ));
289 int count_A = 0; // sceneario QLA,QRB supported
290 int count_B = 0; // sceneario QLB,QRA supported
292 int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
293 int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
295 for (int i = 0; i < numIters; i++) {
296 //random sampling with replacement.
298 if (m->control_pressed) { return 0; }
300 vector<snps> selectedLeft;
302 for (int j = 0; j < numLeft; j++) {
303 int index = int(rand() % left.size());
304 selectedLeft.push_back(left[index]);
307 vector<snps> selectedRight;
308 for (int j = 0; j < numRight; j++) {
309 int index = int(rand() % right.size());
310 selectedRight.push_back(right[index]);
313 /* A ------------------------------------------
315 # Q ------------------------------------------
318 # Q ------------------------------------------
320 # B ------------------------------------------ */
323 float QLA = snpQA(selectedLeft);
324 float QRA = snpQA(selectedRight);
326 float QLB = snpQB(selectedLeft);
327 float QRB = snpQB(selectedRight);
329 //in original - not used - not sure why?
330 //float ALB = snpAB(selectedLeft);
331 //float ARB = snpAB(selectedRight);
333 if ((QLA > QLB) && (QRB > QRA)) {
337 if ((QLB > QLA) && (QRA > QRB)) {
341 //cout << "selected left snp: \n";
342 //for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].parentAChar; }
344 //for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].queryChar; }
346 //for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].parentBChar; }
348 //cout << "selected right snp: \n";
349 //for (int j = 0; j < selectedRight.size(); j++) { cout << selectedRight[j].parentAChar; }
351 //for (int i = 0; i < selectedRight.size(); i++) { cout << selectedRight[i].queryChar; }
353 //for (int i = 0; i < selectedRight.size(); i++) { cout << selectedRight[i].parentBChar; }
358 //cout << count_A << '\t' << count_B << endl;
360 BSA = (float) count_A / (float) numIters * 100;
361 BSB = (float) count_B / (float) numIters * 100;
362 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
367 catch(exception& e) {
368 m->errorOut(e, "Slayer", "bootstrapSNPS");
372 /***********************************************************************/
373 float Slayer::snpQA(vector<snps> data) {
376 int numIdentical = 0;
378 for (int i = 0; i < data.size(); i++) {
379 if (data[i].parentAChar == data[i].queryChar) {
384 float percentID = (numIdentical / (float) data.size()) * 100;
388 catch(exception& e) {
389 m->errorOut(e, "Slayer", "snpQA");
393 /***********************************************************************/
394 float Slayer::snpQB(vector<snps> data) {
397 int numIdentical = 0;
399 for (int i = 0; i < data.size(); i++) {
400 if (data[i].parentBChar == data[i].queryChar) {
405 float percentID = (numIdentical / (float) data.size()) * 100;
410 catch(exception& e) {
411 m->errorOut(e, "Slayer", "snpQB");
415 /***********************************************************************/
416 float Slayer::snpAB(vector<snps> data) {
418 int numIdentical = 0;
420 for (int i = 0; i < data.size(); i++) {
421 if (data[i].parentAChar == data[i].parentBChar) {
426 float percentID = (numIdentical / (float) data.size()) * 100;
431 catch(exception& e) {
432 m->errorOut(e, "Slayer", "snpAB");
436 /***********************************************************************/
437 float Slayer::computePercentID(string queryAlign, string chimera, int left, int right) {
440 int numIdentical = 0;
443 for (int i = left; i <= right; i++) {
444 if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
445 ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
448 bool charA = false; bool charB = false;
449 if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
450 if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
452 if (charA || charB) {
454 if (charA) { countA++; }
455 if (charB) { countB++; }
457 if (queryAlign[i] == chimera[i]) {
465 float numBases = (countA + countB) /(float) 2;
467 if (numBases == 0) { return 0; }
469 float percentIdentical = (numIdentical/(float)numBases) * 100;
471 return percentIdentical;
474 catch(exception& e) {
475 m->errorOut(e, "Slayer", "computePercentID");
479 /***********************************************************************/
480 //remove columns that contain any gaps
481 map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
485 baseSpots.resize(3); //query, parentA, parentB
487 vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
489 string filterString = (string(seqs[0]->getAligned().length(), '1'));
492 for (int i = 0; i < seqs.size(); i++) {
494 string seqAligned = seqs[i]->getAligned();
496 for (int j = 0; j < seqAligned.length(); j++) {
497 //if this spot is a gap
498 if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; }
502 //zero out spot where any sequences have blanks
503 int numColRemoved = 0;
505 map<int, int> maskMap; maskMap.clear();
507 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
508 if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; }
516 for (int i = 0; i < seqs.size(); i++) {
518 string seqAligned = seqs[i]->getAligned();
519 string newAligned = "";
523 for (int j = 0; j < seqAligned.length(); j++) {
525 if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; }
527 //if this spot is not a gap
528 if (filterString[j] == '1') {
529 newAligned += seqAligned[j];
530 baseSpots[i][count] = baseCount;
535 seqs[i]->setAligned(newAligned);
540 catch(exception& e) {
541 m->errorOut(e, "Slayer", "verticalFilter");
545 /***********************************************************************/