X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=57ed7130916b0e1d810b470fa0552dc5556a1143;hb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;hp=293ee807d5b875728716fddde17cd6c032f318e1;hpb=05a0195e07c42c996592ee1c8abb63adedb7f493;p=mothur.git diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp index 293ee80..57ed713 100644 --- a/chimeraslayer.cpp +++ b/chimeraslayer.cpp @@ -8,181 +8,303 @@ */ #include "chimeraslayer.h" +#include "chimerarealigner.h" +#include "kmerdb.hpp" //*************************************************************************************************************** -ChimeraSlayer::ChimeraSlayer(string filename, string temp) { fastafile = filename; templateFile = temp; } +ChimeraSlayer::ChimeraSlayer(string mode, bool r, string f) : searchMethod(mode), realign(r), fastafile(f) { + decalc = new DeCalculator(); +} //*************************************************************************************************************** - -ChimeraSlayer::~ChimeraSlayer() { +int ChimeraSlayer::doPrep() { try { - for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; } - for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } + + string kmerDBNameLeft; + string kmerDBNameRight; + + //generate the kmerdb to pass to maligner + if (searchMethod == "kmer") { + //leftside + string leftTemplateFileName = "left." + templateFileName; + databaseLeft = new KmerDB(leftTemplateFileName, kmerSize); + kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer"; + ifstream kmerFileTestLeft(kmerDBNameLeft.c_str()); + + if(!kmerFileTestLeft){ + + for (int i = 0; i < templateSeqs.size(); i++) { + + if (m->control_pressed) { return 0; } + + string leftFrag = templateSeqs[i]->getUnaligned(); + leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33)); + + Sequence leftTemp(templateSeqs[i]->getName(), leftFrag); + databaseLeft->addSequence(leftTemp); + } + databaseLeft->generateDB(); + + }else { + databaseLeft->readKmerDB(kmerFileTestLeft); + } + kmerFileTestLeft.close(); + + databaseLeft->setNumSeqs(templateSeqs.size()); + + //rightside + string rightTemplateFileName = "right." + templateFileName; + databaseRight = new KmerDB(rightTemplateFileName, kmerSize); + kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer"; + ifstream kmerFileTestRight(kmerDBNameRight.c_str()); + + if(!kmerFileTestRight){ + + for (int i = 0; i < templateSeqs.size(); i++) { + if (m->control_pressed) { return 0; } + + string rightFrag = templateSeqs[i]->getUnaligned(); + rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66)); + + Sequence rightTemp(templateSeqs[i]->getName(), rightFrag); + databaseRight->addSequence(rightTemp); + } + databaseRight->generateDB(); + + }else { + databaseRight->readKmerDB(kmerFileTestRight); + } + kmerFileTestRight.close(); + + databaseRight->setNumSeqs(templateSeqs.size()); + + } + + int start = time(NULL); + //filter the sequences + //read in all query seqs + ifstream in; + openInputFile(fastafile, in); + + vector tempQuerySeqs; + while(!in.eof()){ + if (m->control_pressed) { for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; } return 0; } + + Sequence* s = new Sequence(in); + gobble(in); + + if (s->getName() != "") { tempQuerySeqs.push_back(s); } + } + in.close(); + + vector temp = templateSeqs; + for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); } + + createFilter(temp, 0.0); //just removed columns where all seqs have a gap + + for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; } + + if (m->control_pressed) { return 0; } + + + //run filter on template + for (int i = 0; i < templateSeqs.size(); i++) { if (m->control_pressed) { return 0; } runFilter(templateSeqs[i]); } + + m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to filter."); m->mothurOutEndLine(); + + return 0; + } catch(exception& e) { - errorOut(e, "ChimeraSlayer", "~ChimeraSlayer"); + m->errorOut(e, "ChimeraSlayer", "doprep"); exit(1); } -} +} +//*************************************************************************************************************** +ChimeraSlayer::~ChimeraSlayer() { delete decalc; if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; } } +//*************************************************************************************************************** +void ChimeraSlayer::printHeader(ostream& out) { + m->mothurOutEndLine(); + m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results."); + m->mothurOutEndLine(); + + out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; +} //*************************************************************************************************************** -void ChimeraSlayer::print(ostream& out) { +int ChimeraSlayer::print(ostream& out, ostream& outAcc) { try { + if (chimeraFlags == "yes") { + string chimeraFlag = "no"; + if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR) + || + (chimeraResults[0].bsb >= minBS && chimeraResults[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + + + if (chimeraFlag == "yes") { + if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) { + m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine(); + outAcc << querySeq->getName() << endl; + } + } + + printBlock(chimeraResults[0], out); + out << endl; + }else { out << querySeq->getName() << "\tno" << endl; } - mothurOutEndLine(); + return 0; - } catch(exception& e) { - errorOut(e, "ChimeraSlayer", "print"); + m->errorOut(e, "ChimeraSlayer", "print"); exit(1); } } - //*************************************************************************************************************** -void ChimeraSlayer::getChimeras() { +int ChimeraSlayer::getChimeras(Sequence* query) { try { + chimeraFlags = "no"; - //read in query sequences and subject sequences - mothurOut("Reading sequences and template file... "); cout.flush(); - querySeqs = readSeqs(fastafile); - templateSeqs = readSeqs(templateFile); - mothurOut("Done."); mothurOutEndLine(); - - int numSeqs = querySeqs.size(); - - //break up file if needed - int linesPerProcess = numSeqs / processors ; - - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - //find breakup of sequences for all times we will Parallelize - if (processors == 1) { lines.push_back(new linePair(0, numSeqs)); } - else { - //fill line pairs - for (int i = 0; i < (processors-1); i++) { - lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess))); - } - //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end - int i = processors - 1; - lines.push_back(new linePair((i*linesPerProcess), numSeqs)); - } - #else - lines.push_back(new linePair(0, numSeqs)); - #endif + //filter query + spotMap = runFilter(query); - if (seqMask != "") { decalc = new DeCalculator(); } //to use below + querySeq = query; //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity - maligner = new Maligner(templateSeqs, numWanted, match, misMatch, 1.01, minSim); - slayer = new Slayer(window, increment, minSim, divR); + maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight); + slayer = new Slayer(window, increment, minSim, divR, iters, minSNP); - for (int i = 0; i < querySeqs.size(); i++) { + if (m->control_pressed) { return 0; } - string chimeraFlag = maligner->getResults(querySeqs[i]); - float percentIdentical = maligner->getPercentID(); - vector Results = maligner->getOutput(); - - cout << querySeqs[4]->getName() << '\t' << chimeraFlag << '\t' << percentIdentical << endl; + string chimeraFlag = maligner->getResults(query, decalc); + if (m->control_pressed) { return 0; } + vector Results = maligner->getOutput(); + + //found in testing realigning only made things worse + if (realign) { + ChimeraReAligner realigner(templateSeqs, match, misMatch); + realigner.reAlign(query, Results); + } + + if (chimeraFlag == "yes") { + //get sequence that were given from maligner results + vector seqs; + map removeDups; + map::iterator itDup; + map parentNameSeq; + map::iterator itSeq; for (int j = 0; j < Results.size(); j++) { - cout << "regionStart = " << Results[j].regionStart << "\tRegionEnd = " << Results[j].regionEnd << "\tName = " << Results[j].parent << "\tPerQP = " << Results[j].queryToParent << "\tLocalPerQP = " << Results[j].queryToParentLocal << "\tdivR = " << Results[j].divR << endl; - + float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal; + //only add if you are not a duplicate + itDup = removeDups.find(Results[j].parent); + if (itDup == removeDups.end()) { //this is not duplicate + removeDups[Results[j].parent] = dist; + parentNameSeq[Results[j].parent] = Results[j].parentAligned; + }else if (dist > itDup->second) { //is this a stronger number for this parent + removeDups[Results[j].parent] = dist; + parentNameSeq[Results[j].parent] = Results[j].parentAligned; + } } - if (chimeraFlag == "yes") { + for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) { + //Sequence* seq = getSequence(itDup->first); //makes copy so you can filter and mask and not effect template + itSeq = parentNameSeq.find(itDup->first); +//cout << itDup->first << itSeq->second << endl; + Sequence* seq = new Sequence(itDup->first, itSeq->second); + + SeqDist member; + member.seq = seq; + member.dist = itDup->second; + + seqs.push_back(member); + } - //get sequence that were given from maligner results - vector seqs; - for (int j = 0; j < Results.size(); j++) { - Sequence* seq = getSequence(Results[j].parent); //makes copy so you can filter and mask and not effect template - - //seq = NULL if error occurred in getSequence - if (seq == NULL) { break; } - else { - SeqDist member; - member.seq = seq; - member.dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal; - seqs.push_back(member); - } + //limit number of parents to explore - default 3 + if (Results.size() > parents) { + //sort by distance + sort(seqs.begin(), seqs.end(), compareSeqDist); + //prioritize larger more similiar sequence fragments + reverse(seqs.begin(), seqs.end()); + + for (int k = seqs.size()-1; k > (parents-1); k--) { + delete seqs[k].seq; + seqs.pop_back(); } + } - //limit number of parents to explore - default 5 - if (Results.size() > parents) { - //sort by distance - sort(seqs.begin(), seqs.end(), compareSeqDist); - //prioritize larger more similiar sequence fragments - reverse(seqs.begin(), seqs.end()); - - for (int k = seqs.size()-1; k > (parents-1); k--) { - delete seqs[k].seq; - seqs.pop_back(); - } - } - - //put seqs into vector to send to slayer - vector seqsForSlayer; - for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); } + //put seqs into vector to send to slayer + vector seqsForSlayer; + for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); } - //mask then send to slayer... - if (seqMask != "") { - decalc->setMask(seqMask); - - //mask querys - decalc->runMask(querySeqs[i]); - - //mask parents - for (int k = 0; k < seqsForSlayer.size(); k++) { - decalc->runMask(seqsForSlayer[k]); - } - - } + //mask then send to slayer... + if (seqMask != "") { + decalc->setMask(seqMask); - //send to slayer - slayer->getResults(querySeqs[i], seqsForSlayer); + //mask querys + decalc->runMask(query); - //free memory - for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } + //mask parents + for (int k = 0; k < seqsForSlayer.size(); k++) { + decalc->runMask(seqsForSlayer[k]); + } + + spotMap = decalc->getMaskMap(); } - } - //free memory - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } - - if (seqMask != "") { - delete decalc; - } - + if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; } + + //send to slayer + chimeraFlags = slayer->getResults(query, seqsForSlayer); + if (m->control_pressed) { return 0; } + chimeraResults = slayer->getOutput(); + //free memory + for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } + } + + delete maligner; + delete slayer; + + return 0; } catch(exception& e) { - errorOut(e, "ChimeraSlayer", "getChimeras"); + m->errorOut(e, "ChimeraSlayer", "getChimeras"); exit(1); } } //*************************************************************************************************************** -Sequence* ChimeraSlayer::getSequence(string name) { - try{ - Sequence* temp; - - //look through templateSeqs til you find it - int spot = -1; - for (int i = 0; i < templateSeqs.size(); i++) { - if (name == templateSeqs[i]->getName()) { - spot = i; - break; - } - } +void ChimeraSlayer::printBlock(data_struct data, ostream& out){ + try { + //out << "Name\tParentA\tParentB\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; + + out << querySeq->getName() << '\t'; + out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t'; + //out << "Left Window: " << spotMap[data.winLStart] << " " << spotMap[data.winLEnd] << endl; + //out << "Right Window: " << spotMap[data.winRStart] << " " << spotMap[data.winREnd] << endl; + + out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t'; + out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t'; + + out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t'; - if(spot == -1) { mothurOut("Error: Could not find sequence in chimeraSlayer."); mothurOutEndLine(); return NULL; } + //out << "Similarity of parents: " << data.ab << endl; + //out << "Similarity of query to parentA: " << data.qa << endl; + //out << "Similarity of query to parentB: " << data.qb << endl; - temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned()); - return temp; + //out << "Per_id(QL,A): " << data.qla << endl; + //out << "Per_id(QL,B): " << data.qlb << endl; + //out << "Per_id(QR,A): " << data.qra << endl; + //out << "Per_id(QR,B): " << data.qrb << endl; + + + //out << "DeltaL: " << (data.qla - data.qlb) << endl; + //out << "DeltaR: " << (data.qra - data.qrb) << endl; + } catch(exception& e) { - errorOut(e, "ChimeraSlayer", "getSequence"); + m->errorOut(e, "ChimeraSlayer", "printBlock"); exit(1); } } //*************************************************************************************************************** - -