X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=f834db1db319badab0ddb70cde9e54c7dbb3193f;hb=1cf188b912d6da8f2cd03dd71cecef664a699c1a;hp=b393194bbc3a4c89fd2ae8ea3f7f7ba67f84b927;hpb=9ada98592a54c82d08f3d46c9b1d8c3e472a922d;p=mothur.git diff --git a/maligner.cpp b/maligner.cpp index b393194..f834db1 100644 --- a/maligner.cpp +++ b/maligner.cpp @@ -8,12 +8,14 @@ */ #include "maligner.h" -#include "database.hpp" -#include "blastdb.hpp" -/***********************************************************************/ -Maligner::Maligner(vector temp, int num, int match, int misMatch, float div, int ms, int minCov, string mode) : - db(temp), numWanted(num), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov), searchMethod(mode) {} +/***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight +Maligner::Maligner(vector temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) { + //numWanted(num), , searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight) + + m = MothurOut::getInstance(); + +} /***********************************************************************/ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { try { @@ -25,11 +27,10 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { string chimera; - if (searchMethod != "blast") { - //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate - refSeqs = decalc->findClosest(query, db, numWanted); - }else{ - refSeqs = getBlastSeqs(query, numWanted); + //copy refSeqs so that filter does not effect original + for(int i = 0; i < db.size(); i++) { + Sequence* newSeq = new Sequence(db[i]->getName(), db[i]->getAligned()); + refSeqs.push_back(newSeq); } refSeqs = minCoverageFilter(refSeqs); @@ -41,19 +42,21 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { } int chimeraPenalty = computeChimeraPenalty(); - + //fills outputResults chimera = chimeraMaligner(chimeraPenalty, decalc); + if (m->control_pressed) { return chimera; } //free memory delete query; + for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } return chimera; } catch(exception& e) { - errorOut(e, "Maligner", "getResults"); + m->errorOut(e, "Maligner", "getResults"); exit(1); } } @@ -66,32 +69,58 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { //trims seqs to first non gap char in all seqs and last non gap char in all seqs spotMap = decalc->trimSeqs(query, refSeqs); + //you trimmed the whole sequence, skip + if (query->getAligned() == "") { return "no"; } + vector temp = refSeqs; temp.push_back(query); - + verticalFilter(temp); + + //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl << refSeqs[i]->getAligned() << endl; } vector< vector > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes + if (m->control_pressed) { return chimera; } + fillScoreMatrix(matrix, refSeqs, chimeraPenalty); vector path = extractHighestPath(matrix); + if (m->control_pressed) { return chimera; } + vector trace = mapTraceRegionsToAlignment(path, refSeqs); if (trace.size() > 1) { chimera = "yes"; } - else { chimera = "no"; } + else { chimera = "no"; return chimera; } int traceStart = path[0].col; - int traceEnd = path[path.size()-1].col; - + int traceEnd = path[path.size()-1].col; string queryInRange = query->getAligned(); - queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1)); - + queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart)); + string chimeraSeq = constructChimericSeq(trace, refSeqs); percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq); + /* + vector trace = extractHighestPath(matrix); + + //cout << "traces\n"; + //for(int i=0;igetName() << endl; + //} + + if (trace.size() > 1) { chimera = "yes"; } + else { chimera = "no"; return chimera; } + + int traceStart = trace[0].col; + int traceEnd = trace[trace.size()-1].oldCol; + string queryInRange = query->getAligned(); + queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));*/ + + if (m->control_pressed) { return chimera; } + //save output results for (int i = 0; i < trace.size(); i++) { int regionStart = trace[i].col; @@ -101,32 +130,35 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { results temp; temp.parent = refSeqs[seqIndex]->getName(); + temp.parentAligned = db[seqIndex]->getAligned(); temp.nastRegionStart = spotMap[regionStart]; temp.nastRegionEnd = spotMap[regionEnd]; temp.regionStart = regionStart; temp.regionEnd = regionEnd; string parentInRange = refSeqs[seqIndex]->getAligned(); - parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1)); + parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart)); temp.queryToParent = computePercentID(queryInRange, parentInRange); temp.divR = (percentIdenticalQueryChimera / temp.queryToParent); - + string queryInRegion = query->getAligned(); - queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart+1)); + queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart)); string parentInRegion = refSeqs[seqIndex]->getAligned(); - parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1)); + parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart)); temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion); - + +// cout << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl; + outputResults.push_back(temp); } - + return chimera; } catch(exception& e) { - errorOut(e, "Maligner", "chimeraMaligner"); + m->errorOut(e, "Maligner", "chimeraMaligner"); exit(1); } } @@ -162,13 +194,15 @@ vector Maligner::minCoverageFilter(vector ref){ //if coverage above minimum if (coverage > minCoverage) { newRefs.push_back(ref[i]); + }else { + delete ref[i]; } } return newRefs; } catch(exception& e) { - errorOut(e, "Maligner", "minCoverageFilter"); + m->errorOut(e, "Maligner", "minCoverageFilter"); exit(1); } } @@ -178,14 +212,16 @@ int Maligner::computeChimeraPenalty() { try { int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases()); - + +// if(numAllowable < 1){ numAllowable = 1; } + int penalty = int(numAllowable + 1) * misMatchPenalty; - + return penalty; } catch(exception& e) { - errorOut(e, "Maligner", "computeChimeraPenalty"); + m->errorOut(e, "Maligner", "computeChimeraPenalty"); exit(1); } } @@ -237,7 +273,7 @@ void Maligner::verticalFilter(vector seqs) { spotMap = newMap; } catch(exception& e) { - errorOut(e, "Maligner", "verticalFilter"); + m->errorOut(e, "Maligner", "verticalFilter"); exit(1); } } @@ -245,9 +281,9 @@ void Maligner::verticalFilter(vector seqs) { vector< vector > Maligner::buildScoreMatrix(int cols, int rows) { try{ - vector< vector > m; m.resize(rows); + vector< vector > m(rows); - for (int i = 0; i < m.size(); i++) { + for (int i = 0; i < rows; i++) { for (int j = 0; j < cols; j++) { //initialize each cell @@ -264,12 +300,14 @@ vector< vector > Maligner::buildScoreMatrix(int cols, int rows) { return m; } catch(exception& e) { - errorOut(e, "Maligner", "buildScoreMatrix"); + m->errorOut(e, "Maligner", "buildScoreMatrix"); exit(1); } } + //*************************************************************************************************************** -void Maligner::fillScoreMatrix(vector >& m, vector seqs, int penalty) { + +void Maligner::fillScoreMatrix(vector >& ms, vector seqs, int penalty) { try{ //get matrix dimensions @@ -283,11 +321,14 @@ void Maligner::fillScoreMatrix(vector >& m, vector >& m, vector m[i][j].score) { - m[i][j].score = sumScore; - m[i][j].prev = prevIndex; + if (sumScore > ms[i][j].score) { + ms[i][j].score = sumScore; + ms[i][j].prev = prevIndex; } } } } + /* for(int i=0;igetName(); + for(int j=0;jgetName() << endl << seqs[i]->getAligned() << endl << endl; + if ((seqs[i]->getName() == "S000003470") || (seqs[i]->getName() == "S000383265") || (seqs[i]->getName() == "7000004128191054")) { + for(int j=0;jgetName(); + for(int j=0;jerrorOut(e, "Maligner", "fillScoreMatrix"); exit(1); } } //*************************************************************************************************************** -vector Maligner::extractHighestPath(vector > m) { +vector Maligner::extractHighestPath(vector > ms) { try { - + //get matrix dimensions int numCols = query->getAligned().length(); - int numRows = m.size(); - - + int numRows = ms.size(); + + //find highest score scoring matrix score_struct highestStruct; int highestScore = 0; for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { - if (m[i][j].score > highestScore) { - highestScore = m[i][j].score; - highestStruct = m[i][j]; + if (ms[i][j].score > highestScore) { + highestScore = ms[i][j].score; + highestStruct = ms[i][j]; } } } - + vector path; int rowIndex = highestStruct.row; @@ -362,7 +434,7 @@ vector Maligner::extractHighestPath(vector > int score = highestStruct.score; while (pos >= 0 && score > 0) { - score_struct temp = m[rowIndex][pos]; + score_struct temp = ms[rowIndex][pos]; score = temp.score; if (score > 0) { path.push_back(temp); } @@ -370,18 +442,153 @@ vector Maligner::extractHighestPath(vector > rowIndex = temp.prev; pos--; } - + reverse(path.begin(), path.end()); - + return path; } catch(exception& e) { - errorOut(e, "Maligner", "extractHighestPath"); + m->errorOut(e, "Maligner", "extractHighestPath"); + exit(1); + } +} +//*************************************************************************************************************** +vector Maligner::mapTraceRegionsToAlignment(vector path, vector seqs) { + try { + vector trace; + + int region_index = path[0].row; + int region_start = path[0].col; + + for (int i = 1; i < path.size(); i++) { + + int next_region_index = path[i].row; + + if (next_region_index != region_index) { + + // add trace region + int col_index = path[i].col; + trace_struct temp; + temp.col = region_start; + temp.oldCol = col_index-1; + temp.row = region_index; + + trace.push_back(temp); + + region_index = path[i].row; + region_start = col_index; + } + } + + // get last one + trace_struct temp; + temp.col = region_start; + temp.oldCol = path[path.size()-1].col; + temp.row = region_index; + trace.push_back(temp); + + return trace; + + } + catch(exception& e) { + m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment"); exit(1); } } + +/*************************************************************************************************************** + +vector Maligner::extractHighestPath(vector > ms) { + try { + + + //get matrix dimensions + int numCols = query->getAligned().length(); + int numRows = ms.size(); + + + //find highest score scoring matrix + vector highestStruct; + int highestScore = 0; + + for (int i = 0; i < numRows; i++) { + for (int j = 0; j < numCols; j++) { + if (ms[i][j].score > highestScore) { + highestScore = ms[i][j].score; + highestStruct.resize(0); + highestStruct.push_back(ms[i][j]); + } + else if(ms[i][j].score == highestScore){ + highestStruct.push_back(ms[i][j]); + } + } + } + + //cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl; + + vector maxTrace; + double maxPercentIdenticalQueryAntiChimera = 0; + + for(int i=0;i path; + + int rowIndex = highestStruct[i].row; + int pos = highestStruct[i].col; + int score = highestStruct[i].score; + + while (pos >= 0 && score > 0) { + score_struct temp = ms[rowIndex][pos]; + score = temp.score; + + if (score > 0) { path.push_back(temp); } + + rowIndex = temp.prev; + pos--; + } + + reverse(path.begin(), path.end()); + + vector trace = mapTraceRegionsToAlignment(path, refSeqs); + + //cout << "traces\n"; + //for(int j=0;jgetName() << endl; + //} + + int traceStart = path[0].col; + int traceEnd = path[path.size()-1].col; +// cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl; + + string queryInRange = query->getAligned(); + queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1)); +// cout << "here" << endl; + string chimeraSeq = constructChimericSeq(trace, refSeqs); + string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs); + + percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq); + double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq); +// cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl; + + if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){ + maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera; + maxTrace = trace; + } + } +// cout << maxPercentIdenticalQueryAntiChimera << endl; + return maxTrace; + + + } + catch(exception& e) { + m->errorOut(e, "Maligner", "extractHighestPath"); + exit(1); + } +} + //*************************************************************************************************************** + vector Maligner::mapTraceRegionsToAlignment(vector path, vector seqs) { try { vector trace; @@ -416,56 +623,106 @@ vector Maligner::mapTraceRegionsToAlignment(vector p temp.row = region_index; trace.push_back(temp); +// cout << endl; +// cout << trace.size() << endl; +// for(int i=0;igetName() << endl; +// } +// cout << endl; + return trace; } catch(exception& e) { - errorOut(e, "Maligner", "mapTraceRegionsToAlignment"); + m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment"); exit(1); } } +*/ //*************************************************************************************************************** + string Maligner::constructChimericSeq(vector trace, vector seqs) { try { string chimera = ""; for (int i = 0; i < trace.size(); i++) { +// cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl; + string seqAlign = seqs[trace[i].row]->getAligned(); seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1)); chimera += seqAlign; } - + + if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); } return chimera; } catch(exception& e) { - errorOut(e, "Maligner", "constructChimericSeq"); + m->errorOut(e, "Maligner", "constructChimericSeq"); + exit(1); + } +} + +//*************************************************************************************************************** + +string Maligner::constructAntiChimericSeq(vector trace, vector seqs) { + try { + string antiChimera = ""; + + for (int i = 0; i < trace.size(); i++) { +// cout << i << '\t' << (trace.size() - i - 1) << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl; + + int oppositeIndex = trace.size() - i - 1; + + string seqAlign = seqs[trace[oppositeIndex].row]->getAligned(); + seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1)); + antiChimera += seqAlign; + } + + return antiChimera; + } + catch(exception& e) { + m->errorOut(e, "Maligner", "constructChimericSeq"); exit(1); } } + //*************************************************************************************************************** float Maligner::computePercentID(string queryAlign, string chimera) { try { if (queryAlign.length() != chimera.length()) { - mothurOut("Error, alignment strings are of different lengths: "); mothurOutEndLine(); - mothurOut(toString(queryAlign.length())); mothurOutEndLine(); mothurOutEndLine(); mothurOutEndLine(); mothurOutEndLine(); - mothurOut(toString(chimera.length())); mothurOutEndLine(); + m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine(); + m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine(); + m->mothurOut(toString(chimera.length())); m->mothurOutEndLine(); return -1.0; } - - int numBases = 0; int numIdentical = 0; - + int countA = 0; + int countB = 0; for (int i = 0; i < queryAlign.length(); i++) { - if ((isalpha(queryAlign[i])) || (isalpha(chimera[i]))) { - numBases++; - if (queryAlign[i] == chimera[i]) { - numIdentical++; + 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; @@ -474,69 +731,8 @@ float Maligner::computePercentID(string queryAlign, string chimera) { } catch(exception& e) { - errorOut(e, "Maligner", "computePercentID"); + m->errorOut(e, "Maligner", "computePercentID"); exit(1); } } //*************************************************************************************************************** -vector Maligner::getBlastSeqs(Sequence* q, int num) { - try { - //generate blastdb - Database* database = new BlastDB(-2.0, -1.0, matchScore, misMatchPenalty); - for (int i = 0; i < db.size(); i++) { database->addSequence(*db[i]); } - database->generateDB(); - database->setNumSeqs(db.size()); - - //get parts of query - string queryUnAligned = q->getUnaligned(); - string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence - string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence - - Sequence* queryLeft = new Sequence(q->getName(), leftQuery); - Sequence* queryRight = new Sequence(q->getName(), rightQuery); - - vector tempIndexesRight = database->findClosestMegaBlast(queryRight, num+1); - vector tempIndexesLeft = database->findClosestMegaBlast(queryLeft, num+1); - - //merge results - map seen; - map::iterator it; - - vector mergedResults; - for (int i = 0; i < tempIndexesLeft.size(); i++) { - //add left if you havent already - it = seen.find(tempIndexesLeft[i]); - if (it == seen.end()) { - mergedResults.push_back(tempIndexesLeft[i]); - seen[tempIndexesLeft[i]] = tempIndexesLeft[i]; - } - - //add right if you havent already - it = seen.find(tempIndexesRight[i]); - if (it == seen.end()) { - mergedResults.push_back(tempIndexesRight[i]); - seen[tempIndexesRight[i]] = tempIndexesRight[i]; - } - } - - - vector refResults; - for (int i = 0; i < numWanted; i++) { - Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); - refResults.push_back(temp); - } - - delete queryRight; - delete queryLeft; - delete database; - - return refResults; - } - catch(exception& e) { - errorOut(e, "Maligner", "getBlastSeqs"); - exit(1); - } -} - -//*************************************************************************************************************** -