5 * Created by westcott on 9/23/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
12 /***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight
13 Maligner::Maligner(vector<Sequence*> temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) {
14 //numWanted(num), , searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight)
16 m = MothurOut::getInstance();
19 /***********************************************************************/
20 string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
23 outputResults.clear();
25 //make copy so trimming doesn't destroy query from calling class - remember to deallocate
26 query = new Sequence(q->getName(), q->getAligned());
30 //copy refSeqs so that filter does not effect original
31 for(int i = 0; i < db.size(); i++) {
32 Sequence* newSeq = new Sequence(db[i]->getName(), db[i]->getAligned());
33 refSeqs.push_back(newSeq);
36 refSeqs = minCoverageFilter(refSeqs);
38 if (refSeqs.size() < 2) {
39 for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
40 percentIdenticalQueryChimera = 0.0;
44 int chimeraPenalty = computeChimeraPenalty();
47 chimera = chimeraMaligner(chimeraPenalty, decalc);
49 if (m->control_pressed) { return chimera; }
54 for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
59 m->errorOut(e, "Maligner", "getResults");
63 /***********************************************************************/
64 string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
69 //trims seqs to first non gap char in all seqs and last non gap char in all seqs
70 spotMap = decalc->trimSeqs(query, refSeqs);
72 //you trimmed the whole sequence, skip
73 if (query->getAligned() == "") { return "no"; }
75 vector<Sequence*> temp = refSeqs;
76 temp.push_back(query);
80 //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl << refSeqs[i]->getAligned() << endl; }
82 vector< vector<score_struct> > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes
84 if (m->control_pressed) { return chimera; }
86 fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
88 vector<score_struct> path = extractHighestPath(matrix);
90 if (m->control_pressed) { return chimera; }
92 vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
94 if (trace.size() > 1) { chimera = "yes"; }
95 else { chimera = "no"; return chimera; }
97 int traceStart = path[0].col;
98 int traceEnd = path[path.size()-1].col;
99 string queryInRange = query->getAligned();
100 queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));
102 string chimeraSeq = constructChimericSeq(trace, refSeqs);
104 percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
107 vector<trace_struct> trace = extractHighestPath(matrix);
109 //cout << "traces\n";
110 //for(int i=0;i<trace.size();i++){
111 // cout << trace[i].col << '\t' << trace[i].oldCol << '\t' << refSeqs[trace[i].row]->getName() << endl;
114 if (trace.size() > 1) { chimera = "yes"; }
115 else { chimera = "no"; return chimera; }
117 int traceStart = trace[0].col;
118 int traceEnd = trace[trace.size()-1].oldCol;
119 string queryInRange = query->getAligned();
120 queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));*/
122 if (m->control_pressed) { return chimera; }
124 //save output results
125 for (int i = 0; i < trace.size(); i++) {
126 int regionStart = trace[i].col;
127 int regionEnd = trace[i].oldCol;
128 int seqIndex = trace[i].row;
132 temp.parent = refSeqs[seqIndex]->getName();
133 temp.parentAligned = db[seqIndex]->getAligned();
134 temp.nastRegionStart = spotMap[regionStart];
135 temp.nastRegionEnd = spotMap[regionEnd];
136 temp.regionStart = regionStart;
137 temp.regionEnd = regionEnd;
139 string parentInRange = refSeqs[seqIndex]->getAligned();
140 parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart));
142 temp.queryToParent = computePercentID(queryInRange, parentInRange);
143 temp.divR = (percentIdenticalQueryChimera / temp.queryToParent);
145 string queryInRegion = query->getAligned();
146 queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart));
148 string parentInRegion = refSeqs[seqIndex]->getAligned();
149 parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart));
151 temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
153 // cout << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl;
154 outputResults.push_back(temp);
159 catch(exception& e) {
160 m->errorOut(e, "Maligner", "chimeraMaligner");
164 /***********************************************************************/
165 //removes top matches that do not have minimum coverage with query.
166 vector<Sequence*> Maligner::minCoverageFilter(vector<Sequence*> ref){
168 vector<Sequence*> newRefs;
170 string queryAligned = query->getAligned();
172 for (int i = 0; i < ref.size(); i++) {
174 string refAligned = ref[i]->getAligned();
180 for (int j = 0; j < queryAligned.length(); j++) {
182 if (isalpha(queryAligned[j])) {
185 if (isalpha(refAligned[j])) {
191 int coverage = ((numCovered/(float)numBases)*100);
193 //if coverage above minimum
194 if (coverage > minCoverage) {
195 newRefs.push_back(ref[i]);
203 catch(exception& e) {
204 m->errorOut(e, "Maligner", "minCoverageFilter");
208 /***********************************************************************/
209 // a breakpoint should yield fewer mismatches than this number with respect to the best parent sequence.
210 int Maligner::computeChimeraPenalty() {
213 int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases());
215 // if(numAllowable < 1){ numAllowable = 1; }
217 int penalty = int(numAllowable + 1) * misMatchPenalty;
222 catch(exception& e) {
223 m->errorOut(e, "Maligner", "computeChimeraPenalty");
227 /***********************************************************************/
228 //this is a vertical filter
229 void Maligner::verticalFilter(vector<Sequence*> seqs) {
231 vector<int> gaps; gaps.resize(query->getAligned().length(), 0);
233 string filterString = (string(query->getAligned().length(), '1'));
236 for (int i = 0; i < seqs.size(); i++) {
238 string seqAligned = seqs[i]->getAligned();
240 for (int j = 0; j < seqAligned.length(); j++) {
241 //if this spot is a gap
242 if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; }
246 //zero out spot where all sequences have blanks
247 int numColRemoved = 0;
248 for(int i = 0; i < seqs[0]->getAligned().length(); i++){
249 if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
252 map<int, int> newMap;
254 for (int i = 0; i < seqs.size(); i++) {
256 string seqAligned = seqs[i]->getAligned();
257 string newAligned = "";
260 for (int j = 0; j < seqAligned.length(); j++) {
261 //if this spot is not a gap
262 if (filterString[j] == '1') {
263 newAligned += seqAligned[j];
264 newMap[count] = spotMap[j];
269 seqs[i]->setAligned(newAligned);
274 catch(exception& e) {
275 m->errorOut(e, "Maligner", "verticalFilter");
279 //***************************************************************************************************************
280 vector< vector<score_struct> > Maligner::buildScoreMatrix(int cols, int rows) {
283 vector< vector<score_struct> > m(rows);
285 for (int i = 0; i < rows; i++) {
286 for (int j = 0; j < cols; j++) {
288 //initialize each cell
291 temp.score = -9999999;
295 m[i].push_back(temp);
301 catch(exception& e) {
302 m->errorOut(e, "Maligner", "buildScoreMatrix");
307 //***************************************************************************************************************
309 void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence*> seqs, int penalty) {
312 //get matrix dimensions
313 int numCols = query->getAligned().length();
314 int numRows = seqs.size();
316 //initialize first col
317 string queryAligned = query->getAligned();
318 for (int i = 0; i < numRows; i++) {
319 string subjectAligned = seqs[i]->getAligned();
322 if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) {
324 // ms[i][0].mismatches = 0;
325 }else if (queryAligned[0] == subjectAligned[0]) { //|| subjectAligned[0] == 'N')
326 ms[i][0].score = matchScore;
327 // ms[i][0].mismatches = 0;
330 // ms[i][0].mismatches = 1;
334 //fill rest of matrix
335 for (int j = 1; j < numCols; j++) { //iterate through matrix columns
337 for (int i = 0; i < numRows; i++) { //iterate through matrix rows
339 string subjectAligned = seqs[i]->getAligned();
341 int matchMisMatchScore = 0;
343 if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
345 }else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
346 //matchMisMatchScore = matchScore;
348 }else if (queryAligned[j] == subjectAligned[j]) {
349 matchMisMatchScore = matchScore;
350 // ms[i][j].mismatches = ms[i][j-1].mismatches;
351 }else if (queryAligned[j] != subjectAligned[j]) {
352 matchMisMatchScore = misMatchPenalty;
353 // ms[i][j].mismatches = ms[i][j-1].mismatches + 1;
356 //compute score based on previous columns scores
357 for (int prevIndex = 0; prevIndex < numRows; prevIndex++) { //iterate through rows
359 int sumScore = matchMisMatchScore + ms[prevIndex][j-1].score;
361 //you are not at yourself
362 if (prevIndex != i) { sumScore += penalty; }
363 if (sumScore < 0) { sumScore = 0; }
365 if (sumScore > ms[i][j].score) {
366 ms[i][j].score = sumScore;
367 ms[i][j].prev = prevIndex;
373 /* for(int i=0;i<numRows;i++){
374 cout << seqs[i]->getName();
375 for(int j=0;j<numCols;j++){
376 cout << '\t' << ms[i][j].mismatches;
381 /*cout << numRows << '\t' << numCols << endl;
382 for(int i=0;i<numRows;i++){
383 cout << seqs[i]->getName() << endl << seqs[i]->getAligned() << endl << endl;
384 if ((seqs[i]->getName() == "S000003470") || (seqs[i]->getName() == "S000383265") || (seqs[i]->getName() == "7000004128191054")) {
385 for(int j=0;j<numCols;j++){
386 cout << '\t' << ms[i][j].score;
392 /*for(int i=0;i<numRows;i++){
393 cout << seqs[i]->getName();
394 for(int j=0;j<numCols;j++){
395 cout << '\t' << ms[i][j].prev;
402 catch(exception& e) {
403 m->errorOut(e, "Maligner", "fillScoreMatrix");
407 //***************************************************************************************************************
408 vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
411 //get matrix dimensions
412 int numCols = query->getAligned().length();
413 int numRows = ms.size();
416 //find highest score scoring matrix
417 score_struct highestStruct;
418 int highestScore = 0;
420 for (int i = 0; i < numRows; i++) {
421 for (int j = 0; j < numCols; j++) {
422 if (ms[i][j].score > highestScore) {
423 highestScore = ms[i][j].score;
424 highestStruct = ms[i][j];
429 vector<score_struct> path;
431 int rowIndex = highestStruct.row;
432 int pos = highestStruct.col;
433 int score = highestStruct.score;
435 while (pos >= 0 && score > 0) {
436 score_struct temp = ms[rowIndex][pos];
439 if (score > 0) { path.push_back(temp); }
441 rowIndex = temp.prev;
445 reverse(path.begin(), path.end());
450 catch(exception& e) {
451 m->errorOut(e, "Maligner", "extractHighestPath");
455 //***************************************************************************************************************
456 vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
458 vector<trace_struct> trace;
460 int region_index = path[0].row;
461 int region_start = path[0].col;
463 for (int i = 1; i < path.size(); i++) {
465 int next_region_index = path[i].row;
467 if (next_region_index != region_index) {
470 int col_index = path[i].col;
472 temp.col = region_start;
473 temp.oldCol = col_index-1;
474 temp.row = region_index;
476 trace.push_back(temp);
478 region_index = path[i].row;
479 region_start = col_index;
485 temp.col = region_start;
486 temp.oldCol = path[path.size()-1].col;
487 temp.row = region_index;
488 trace.push_back(temp);
493 catch(exception& e) {
494 m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
499 /***************************************************************************************************************
501 vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
505 //get matrix dimensions
506 int numCols = query->getAligned().length();
507 int numRows = ms.size();
510 //find highest score scoring matrix
511 vector<score_struct> highestStruct;
512 int highestScore = 0;
514 for (int i = 0; i < numRows; i++) {
515 for (int j = 0; j < numCols; j++) {
516 if (ms[i][j].score > highestScore) {
517 highestScore = ms[i][j].score;
518 highestStruct.resize(0);
519 highestStruct.push_back(ms[i][j]);
521 else if(ms[i][j].score == highestScore){
522 highestStruct.push_back(ms[i][j]);
527 //cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl;
529 vector<trace_struct> maxTrace;
530 double maxPercentIdenticalQueryAntiChimera = 0;
532 for(int i=0;i<highestStruct.size();i++){
534 vector<score_struct> path;
536 int rowIndex = highestStruct[i].row;
537 int pos = highestStruct[i].col;
538 int score = highestStruct[i].score;
540 while (pos >= 0 && score > 0) {
541 score_struct temp = ms[rowIndex][pos];
544 if (score > 0) { path.push_back(temp); }
546 rowIndex = temp.prev;
550 reverse(path.begin(), path.end());
552 vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
554 //cout << "traces\n";
555 //for(int j=0;j<trace.size();j++){
556 // cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
559 int traceStart = path[0].col;
560 int traceEnd = path[path.size()-1].col;
561 // cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
563 string queryInRange = query->getAligned();
564 queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
565 // cout << "here" << endl;
566 string chimeraSeq = constructChimericSeq(trace, refSeqs);
567 string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs);
569 percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
570 double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq);
571 // cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl;
573 if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
574 maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
578 // cout << maxPercentIdenticalQueryAntiChimera << endl;
583 catch(exception& e) {
584 m->errorOut(e, "Maligner", "extractHighestPath");
589 //***************************************************************************************************************
591 vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
593 vector<trace_struct> trace;
595 int region_index = path[0].row;
596 int region_start = path[0].col;
598 for (int i = 1; i < path.size(); i++) {
600 int next_region_index = path[i].row;
602 if (next_region_index != region_index) {
605 int col_index = path[i].col;
607 temp.col = region_start;
608 temp.oldCol = col_index-1;
609 temp.row = region_index;
611 trace.push_back(temp);
613 region_index = path[i].row;
614 region_start = col_index;
620 temp.col = region_start;
621 temp.oldCol = path[path.size()-1].col;
622 temp.row = region_index;
623 trace.push_back(temp);
626 // cout << trace.size() << endl;
627 // for(int i=0;i<trace.size();i++){
628 // cout << seqs[trace[i].row]->getName() << endl;
635 catch(exception& e) {
636 m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
641 //***************************************************************************************************************
643 string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
647 for (int i = 0; i < trace.size(); i++) {
648 // cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
650 string seqAlign = seqs[trace[i].row]->getAligned();
651 seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
655 if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); }
658 catch(exception& e) {
659 m->errorOut(e, "Maligner", "constructChimericSeq");
664 //***************************************************************************************************************
666 string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
668 string antiChimera = "";
670 for (int i = 0; i < trace.size(); i++) {
671 // cout << i << '\t' << (trace.size() - i - 1) << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
673 int oppositeIndex = trace.size() - i - 1;
675 string seqAlign = seqs[trace[oppositeIndex].row]->getAligned();
676 seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
677 antiChimera += seqAlign;
682 catch(exception& e) {
683 m->errorOut(e, "Maligner", "constructChimericSeq");
688 //***************************************************************************************************************
689 float Maligner::computePercentID(string queryAlign, string chimera) {
692 if (queryAlign.length() != chimera.length()) {
693 m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine();
694 m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine();
695 m->mothurOut(toString(chimera.length())); m->mothurOutEndLine();
699 int numIdentical = 0;
702 for (int i = 0; i < queryAlign.length(); i++) {
703 if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
704 ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
707 bool charA = false; bool charB = false;
708 if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
709 if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
711 if (charA || charB) {
713 if (charA) { countA++; }
714 if (charB) { countB++; }
716 if (queryAlign[i] == chimera[i]) {
723 float numBases = (countA + countB) /(float) 2;
725 if (numBases == 0) { return 0; }
727 float percentIdentical = (numIdentical/(float)numBases) * 100;
729 return percentIdentical;
732 catch(exception& e) {
733 m->errorOut(e, "Maligner", "computePercentID");
737 //***************************************************************************************************************