X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=599c78be2c5c69570cb0d96febfa861f90bb8eb5;hb=75f3178fc8e8cfede019f07689211d18325754a9;hp=c5cc83a4d216b9c5a89eb6f60de8a15e5906d06c;hpb=0571957d68cbbc0e425af1db8e808f826010b9e2;p=mothur.git diff --git a/maligner.cpp b/maligner.cpp index c5cc83a..599c78b 100644 --- a/maligner.cpp +++ b/maligner.cpp @@ -8,23 +8,14 @@ */ #include "maligner.h" -#include "kmerdb.hpp" -#include "blastdb.hpp" -/***********************************************************************/ -Maligner::Maligner(vector temp, int num, int match, int misMatch, float div, int ms, int minCov, string mode, Database* dataLeft, Database* dataRight) : - db(temp), numWanted(num), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov), searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight) { - +/***********************************************************************/ //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(); -// cout << matchScore << '\t' << misMatchPenalty << endl; -// -// matchScore = 1; -// misMatchPenalty = -1; - - } - +} /***********************************************************************/ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { try { @@ -36,21 +27,14 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { string chimera; - if (searchMethod == "distance") { - //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, indexes); - }else if (searchMethod == "blast") { - refSeqs = getBlastSeqs(query, numWanted); //fills indexes - }else if (searchMethod == "kmer") { - refSeqs = getKmerSeqs(query, numWanted); //fills indexes - }else { m->mothurOut("not valid search."); exit(1); } //should never get here - - if (m->control_pressed) { return chimera; } + //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); - - if (refSeqs.size() < 2) { for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } percentIdenticalQueryChimera = 0.0; @@ -58,7 +42,7 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { } int chimeraPenalty = computeChimeraPenalty(); - //cout << "chimeraPenalty = " << chimeraPenalty << endl; + //fills outputResults chimera = chimeraMaligner(chimeraPenalty, decalc); @@ -100,7 +84,26 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { 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"; return chimera; } + + int traceStart = path[0].col; + int traceEnd = path[path.size()-1].col; + string queryInRange = query->getAligned(); + queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart)); + + string chimeraSeq = constructChimericSeq(trace, refSeqs); + + percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq); + + /* vector trace = extractHighestPath(matrix); //cout << "traces\n"; @@ -114,7 +117,7 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { int traceStart = trace[0].col; int traceEnd = trace[trace.size()-1].oldCol; string queryInRange = query->getAligned(); - queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1)); + queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));*/ if (m->control_pressed) { return chimera; } @@ -127,26 +130,27 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { results temp; temp.parent = refSeqs[seqIndex]->getName(); - temp.parentAligned = db[indexes[seqIndex]]->getAligned(); + 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); } @@ -400,8 +404,99 @@ void Maligner::fillScoreMatrix(vector >& ms, vector Maligner::extractHighestPath(vector > ms) { + try { + + //get matrix dimensions + int numCols = query->getAligned().length(); + 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 (ms[i][j].score > highestScore) { + highestScore = ms[i][j].score; + highestStruct = ms[i][j]; + } + } + } + + vector path; + + int rowIndex = highestStruct.row; + int pos = highestStruct.col; + int score = highestStruct.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()); + + return path; + + } + catch(exception& e) { + 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 { @@ -542,7 +637,7 @@ vector Maligner::mapTraceRegionsToAlignment(vector p exit(1); } } - +*/ //*************************************************************************************************************** string Maligner::constructChimericSeq(vector trace, vector seqs) { @@ -556,7 +651,8 @@ string Maligner::constructChimericSeq(vector trace, vectormothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine(); - m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine(); 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; @@ -626,256 +735,3 @@ float Maligner::computePercentID(string queryAlign, string chimera) { } } //*************************************************************************************************************** -vector Maligner::getBlastSeqs(Sequence* q, int num) { - try { - indexes.clear(); - vector refResults; - - //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()+"left", leftQuery); - Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery); - - vector tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1); - vector leftScores = databaseLeft->getSearchScores(); - vector tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1); - vector rightScores = databaseLeft->getSearchScores(); - - //if ((tempIndexesRight.size() == 0) && (tempIndexesLeft.size() == 0)) { m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to process sequence " + q->getName()); m->mothurOutEndLine(); return refResults; } - - vector smaller; - vector smallerScores; - vector larger; - vector largerScores; - - if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; smallerScores = rightScores; larger = tempIndexesLeft; largerScores = leftScores; } - else { smaller = tempIndexesLeft; smallerScores = leftScores; larger = tempIndexesRight; largerScores = rightScores; } - - //for (int i = 0; i < smaller.size(); i++) { cout << "smaller = " << smaller[i] << '\t' << smallerScores[i] << endl; } - //cout << endl; - //for (int i = 0; i < larger.size(); i++) { cout << "larger = " << larger[i] << '\t' << largerScores[i] << endl; } - - //merge results - map seen; - map::iterator it; - float lastSmaller = smallerScores[0]; - float lastLarger = largerScores[0]; - int lasti = 0; - vector mergedResults; - for (int i = 0; i < smaller.size(); i++) { - //add left if you havent already - it = seen.find(smaller[i]); - if (it == seen.end()) { - mergedResults.push_back(smaller[i]); - seen[smaller[i]] = smaller[i]; - lastSmaller = smallerScores[i]; - } - - //add right if you havent already - it = seen.find(larger[i]); - if (it == seen.end()) { - mergedResults.push_back(larger[i]); - seen[larger[i]] = larger[i]; - lastLarger = largerScores[i]; - } - - lasti = i; - //if (mergedResults.size() > num) { break; } - } - - //save lasti for smaller ties below - /*lasti++; - int iSmaller = lasti; - - if (!(mergedResults.size() > num)) { //if we still need more results. - for (int i = smaller.size(); i < larger.size(); i++) { - it = seen.find(larger[i]); - if (it == seen.end()) { - mergedResults.push_back(larger[i]); - seen[larger[i]] = larger[i]; - lastLarger = largerScores[i]; - } - - lasti = i; - if (mergedResults.size() > num) { break; } - } - } - - - //add in any ties from smaller - while (iSmaller < smaller.size()) { - if (smallerScores[iSmaller] == lastSmaller) { - it = seen.find(smaller[iSmaller]); - - if (it == seen.end()) { - mergedResults.push_back(smaller[iSmaller]); - seen[smaller[iSmaller]] = smaller[iSmaller]; - } - } - else { break; } - iSmaller++; - } - - lasti++; - //add in any ties from larger - while (lasti < larger.size()) { - if (largerScores[lasti] == lastLarger) { //is it a tie - it = seen.find(larger[lasti]); - - if (it == seen.end()) { //we haven't already seen it - mergedResults.push_back(larger[lasti]); - seen[larger[lasti]] = larger[lasti]; - } - } - else { break; } - lasti++; - } - */ - - for (int i = smaller.size(); i < larger.size(); i++) { - //add right if you havent already - it = seen.find(larger[i]); - if (it == seen.end()) { - mergedResults.push_back(larger[i]); - seen[larger[i]] = larger[i]; - lastLarger = largerScores[i]; - } - } - numWanted = mergedResults.size(); - - if (mergedResults.size() < numWanted) { numWanted = mergedResults.size(); } -//cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted << endl; - for (int i = 0; i < numWanted; i++) { -//cout << db[mergedResults[i]]->getName() << '\t' << mergedResults[i] << endl; - - if (db[mergedResults[i]]->getName() != q->getName()) { - Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); - refResults.push_back(temp); - indexes.push_back(mergedResults[i]); - //cout << db[mergedResults[i]]->getName() << endl; - } - -//cout << mergedResults[i] << endl; - } -//cout << "done " << q->getName() << endl; - delete queryRight; - delete queryLeft; - - return refResults; - } - catch(exception& e) { - m->errorOut(e, "Maligner", "getBlastSeqs"); - exit(1); - } -} -//*************************************************************************************************************** -vector Maligner::getKmerSeqs(Sequence* q, int num) { - try { - indexes.clear(); - - //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 tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, numWanted); - vector tempIndexesRight = databaseRight->findClosestSequences(queryRight, numWanted); - vector scoresLeft = databaseLeft->getSearchScores(); - vector scoresRight = databaseRight->getSearchScores(); - - //merge results - map seen; - map::iterator it; - float lastRight = scoresRight[0]; - float lastLeft = scoresLeft[0]; - //int lasti = 0; - 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]; - lastLeft = scoresLeft[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]; - lastRight = scoresRight[i]; - } - - //if (mergedResults.size() > numWanted) { lasti = i; break; } //you have enough results - } - - //add in sequences with same distance as last sequence added - /*lasti++; - int i = lasti; - while (i < tempIndexesLeft.size()) { - if (scoresLeft[i] == lastLeft) { - it = seen.find(tempIndexesLeft[i]); - - if (it == seen.end()) { - mergedResults.push_back(tempIndexesLeft[i]); - seen[tempIndexesLeft[i]] = tempIndexesLeft[i]; - } - } - else { break; } - i++; - } - - // cout << "lastRight\t" << lastRight << endl; - //add in sequences with same distance as last sequence added - i = lasti; - while (i < tempIndexesRight.size()) { - if (scoresRight[i] == lastRight) { - it = seen.find(tempIndexesRight[i]); - - if (it == seen.end()) { - mergedResults.push_back(tempIndexesRight[i]); - seen[tempIndexesRight[i]] = tempIndexesRight[i]; - } - } - else { break; } - i++; - }*/ - - numWanted = mergedResults.size(); - - if (numWanted > mergedResults.size()) { - //m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine(); - numWanted = mergedResults.size(); - } - - -//cout << q->getName() << endl; - vector refResults; - for (int i = 0; i < numWanted; i++) { -//cout << db[mergedResults[i]]->getName() << endl; - if (db[mergedResults[i]]->getName() != q->getName()) { - Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); - refResults.push_back(temp); - indexes.push_back(mergedResults[i]); - } - } -//cout << endl; - delete queryRight; - delete queryLeft; - - return refResults; - } - catch(exception& e) { - m->errorOut(e, "Maligner", "getKmerSeqs"); - exit(1); - } -} -//*************************************************************************************************************** -