X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=102db7478223d0027e676304288552a2148966fb;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=38f7abe49bfc7266e6eb4acd123ff057b8780c42;hpb=605ab6fa594317a38f0df7bb6797740c735b2348;p=mothur.git diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp index 38f7abe..102db74 100644 --- a/chimeraslayer.cpp +++ b/chimeraslayer.cpp @@ -14,7 +14,7 @@ //*************************************************************************************************************** ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string mode, int k, int ms, int mms, int win, float div, -int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() { +int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera() { try { fastafile = file; templateFileName = temp; templateSeqs = readSeqs(temp); @@ -34,9 +34,10 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num numWanted = numw; realign = r; trimChimera = trim; + numNoParents = 0; + blastlocation = blas; + threadID = tid; - decalc = new DeCalculator(); - doPrep(); } catch(exception& e) { @@ -45,9 +46,11 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num } } //*************************************************************************************************************** -ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string name, string mode, string abunds, int k, int ms, int mms, int win, float div, - int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() { +//template=self, byGroup parameter used for mpienabled version to read the template as MPI_COMM_SELF instead of MPI_COMM_WORLD +ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map& prior, string mode, int k, int ms, int mms, int win, float div, + int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid, bool bg) : Chimera() { try { + byGroup = bg; fastafile = file; templateSeqs = readSeqs(fastafile); templateFileName = temp; searchMethod = mode; @@ -65,19 +68,27 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string name, s increment = inc; numWanted = numw; realign = r; - includeAbunds = abunds; trimChimera = trim; + priority = prior; + numNoParents = 0; + blastlocation = blas; + threadID = tid; - //read name file and create nameMapRank - readNameFile(name); - - decalc = new DeCalculator(); createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap - //run filter on template - for (int i = 0; i < templateSeqs.size(); i++) { runFilter(templateSeqs[i]); } - + if (searchMethod == "distance") { + //createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap + + //run filter on template copying templateSeqs into filteredTemplateSeqs + for (int i = 0; i < templateSeqs.size(); i++) { + if (m->control_pressed) { break; } + + Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned()); + runFilter(newSeq); + filteredTemplateSeqs.push_back(newSeq); + } + } } catch(exception& e) { m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer"); @@ -85,77 +96,79 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string name, s } } //*************************************************************************************************************** -int ChimeraSlayer::readNameFile(string name) { +//template=self +ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map& prior, string mode, int k, int ms, int mms, int win, float div, + int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera() { try { - ifstream in; - m->openInputFile(name, in); + fastafile = file; templateSeqs = readSeqs(fastafile); + templateFileName = temp; + searchMethod = mode; + kmerSize = k; + match = ms; + misMatch = mms; + window = win; + divR = div; + minSim = minsim; + minCov = mincov; + minBS = minbs; + minSNP = minsnp; + parents = par; + iters = it; + increment = inc; + numWanted = numw; + realign = r; + trimChimera = trim; + priority = prior; + numNoParents = 0; + blastlocation = blas; + threadID = tid; - int maxRank = 0; - int minRank = 10000000; - while(!in.eof()){ - - if (m->control_pressed) { in.close(); return 0; } - - string thisname, repnames; - - in >> thisname; m->gobble(in); //read from first column - in >> repnames; //read from second column - - map >::iterator it = nameMapRank.find(thisname); - if (it == nameMapRank.end()) { - - vector splitRepNames; - m->splitAtComma(repnames, splitRepNames); - - nameMapRank[thisname] = splitRepNames; - - if (splitRepNames.size() > maxRank) { maxRank = splitRepNames.size(); } - if (splitRepNames.size() < minRank) { minRank = splitRepNames.size(); } - - }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); } - - m->gobble(in); - } - in.close(); + createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap - //sanity check to make sure files match - for (int i = 0; i < templateSeqs.size(); i++) { - map >::iterator it = nameMapRank.find(templateSeqs[i]->getName()); + if (searchMethod == "distance") { + //createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap - if (it == nameMapRank.end()) { m->mothurOut("[ERROR]: " + templateSeqs[i]->getName() + " is not in namesfile, but is in fastafile. Every name in fasta file must be in first column of names file."); m->mothurOutEndLine(); m->control_pressed = true; } + //run filter on template copying templateSeqs into filteredTemplateSeqs + for (int i = 0; i < templateSeqs.size(); i++) { + if (m->control_pressed) { break; } + + Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned()); + runFilter(newSeq); + filteredTemplateSeqs.push_back(newSeq); + } } - - if (maxRank == minRank) { m->mothurOut("[ERROR]: all sequences in namesfile have the same abundance, aborting."); m->mothurOutEndLine(); m->control_pressed = true; } - - return 0; - } catch(exception& e) { - m->errorOut(e, "ChimeraSlayer", "readNameFile"); + m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer"); exit(1); } } - //*************************************************************************************************************** int ChimeraSlayer::doPrep() { try { + if (searchMethod == "distance") { + //read in all query seqs + vector tempQuerySeqs = readSeqs(fastafile); - //read in all query seqs - vector tempQuerySeqs = readSeqs(fastafile); + vector temp = templateSeqs; + for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); } - 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 - createFilter(temp, 0.0); //just removed columns where all seqs have a gap + for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; } - 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]); } + if (m->control_pressed) { return 0; } + //run filter on template copying templateSeqs into filteredTemplateSeqs + for (int i = 0; i < templateSeqs.size(); i++) { + if (m->control_pressed) { return 0; } + + Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned()); + runFilter(newSeq); + filteredTemplateSeqs.push_back(newSeq); + } + } string kmerDBNameLeft; string kmerDBNameRight; @@ -258,7 +271,10 @@ int ChimeraSlayer::doPrep() { }else if (searchMethod == "blast") { //generate blastdb - databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch); + databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3, blastlocation, threadID); + + if (m->control_pressed) { return 0; } + for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); } databaseLeft->generateDB(); databaseLeft->setNumSeqs(templateSeqs.size()); @@ -273,47 +289,32 @@ int ChimeraSlayer::doPrep() { } } //*************************************************************************************************************** -vector ChimeraSlayer::getTemplate(Sequence* q) { +vector ChimeraSlayer::getTemplate(Sequence q, vector& userTemplateFiltered) { try { - vector thisTemplate; + //when template=self, the query file is sorted from most abundance to least abundant + //userTemplate grows as the query file is processed by adding sequences that are not chimeric and more abundant + vector userTemplate; - int thisRank; - string thisName = q->getName(); - map >::iterator itRank = nameMapRank.find(thisName); // you will find it because we already sanity checked - thisRank = (itRank->second).size(); - - //create list of names we want to put into the template - set namesToAdd; - for (itRank = nameMapRank.begin(); itRank != nameMapRank.end(); itRank++) { - if (itRank->first != thisName) { - if (includeAbunds == "greaterequal") { - if ((itRank->second).size() >= thisRank) { - //you are more abundant than me or equal to my abundance - for (int i = 0; i < (itRank->second).size(); i++) { - namesToAdd.insert((itRank->second)[i]); - } - } - }else if (includeAbunds == "greater") { - if ((itRank->second).size() > thisRank) { - //you are more abundant than me - for (int i = 0; i < (itRank->second).size(); i++) { - namesToAdd.insert((itRank->second)[i]); - } - } - }else if (includeAbunds == "all") { - //add everyone - for (int i = 0; i < (itRank->second).size(); i++) { - namesToAdd.insert((itRank->second)[i]); - } - } + int myAbund = priority[q.getName()]; + + for (int i = 0; i < templateSeqs.size(); i++) { + + if (m->control_pressed) { return userTemplate; } + + //have I reached a sequence with the same abundance as myself? + if (!(priority[templateSeqs[i]->getName()] > myAbund)) { break; } + + //if its am not chimeric add it + if (chimericSeqs.count(templateSeqs[i]->getName()) == 0) { + userTemplate.push_back(templateSeqs[i]); + if (searchMethod == "distance") { userTemplateFiltered.push_back(filteredTemplateSeqs[i]); } } } - for (int i = 0; i < templateSeqs.size(); i++) { - if (namesToAdd.count(templateSeqs[i]->getName()) != 0) { - thisTemplate.push_back(templateSeqs[i]); - } + //avoids nuisance error from formatdb for making blank blast database + if (userTemplate.size() == 0) { + return userTemplate; } string kmerDBNameLeft; @@ -328,69 +329,72 @@ vector ChimeraSlayer::getTemplate(Sequence* q) { string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName)); databaseLeft = new KmerDB(leftTemplateFileName, kmerSize); #ifdef USE_MPI - for (int i = 0; i < thisTemplate.size(); i++) { + for (int i = 0; i < userTemplate.size(); i++) { - if (m->control_pressed) { return thisTemplate; } + if (m->control_pressed) { return userTemplate; } - string leftFrag = thisTemplate[i]->getUnaligned(); + string leftFrag = userTemplate[i]->getUnaligned(); leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33)); - Sequence leftTemp(thisTemplate[i]->getName(), leftFrag); + Sequence leftTemp(userTemplate[i]->getName(), leftFrag); databaseLeft->addSequence(leftTemp); } databaseLeft->generateDB(); - databaseLeft->setNumSeqs(thisTemplate.size()); + databaseLeft->setNumSeqs(userTemplate.size()); - for (int i = 0; i < thisTemplate.size(); i++) { - if (m->control_pressed) { return thisTemplate; } + for (int i = 0; i < userTemplate.size(); i++) { + if (m->control_pressed) { return userTemplate; } - string rightFrag = thisTemplate[i]->getUnaligned(); + string rightFrag = userTemplate[i]->getUnaligned(); rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66)); - Sequence rightTemp(thisTemplate[i]->getName(), rightFrag); + Sequence rightTemp(userTemplate[i]->getName(), rightFrag); databaseRight->addSequence(rightTemp); } databaseRight->generateDB(); - databaseRight->setNumSeqs(thisTemplate.size()); + databaseRight->setNumSeqs(userTemplate.size()); #else - for (int i = 0; i < thisTemplate.size(); i++) { + for (int i = 0; i < userTemplate.size(); i++) { - if (m->control_pressed) { return thisTemplate; } + if (m->control_pressed) { return userTemplate; } - string leftFrag = thisTemplate[i]->getUnaligned(); + string leftFrag = userTemplate[i]->getUnaligned(); leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33)); - Sequence leftTemp(thisTemplate[i]->getName(), leftFrag); + Sequence leftTemp(userTemplate[i]->getName(), leftFrag); databaseLeft->addSequence(leftTemp); } databaseLeft->generateDB(); - databaseLeft->setNumSeqs(thisTemplate.size()); + databaseLeft->setNumSeqs(userTemplate.size()); - for (int i = 0; i < thisTemplate.size(); i++) { - if (m->control_pressed) { return thisTemplate; } + for (int i = 0; i < userTemplate.size(); i++) { + if (m->control_pressed) { return userTemplate; } - string rightFrag = thisTemplate[i]->getUnaligned(); + string rightFrag = userTemplate[i]->getUnaligned(); rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66)); - Sequence rightTemp(thisTemplate[i]->getName(), rightFrag); + Sequence rightTemp(userTemplate[i]->getName(), rightFrag); databaseRight->addSequence(rightTemp); } databaseRight->generateDB(); - databaseRight->setNumSeqs(thisTemplate.size()); + databaseRight->setNumSeqs(userTemplate.size()); #endif }else if (searchMethod == "blast") { //generate blastdb - databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch); - for (int i = 0; i < thisTemplate.size(); i++) { if (m->control_pressed) { return thisTemplate; } databaseLeft->addSequence(*thisTemplate[i]); } + databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3, blastlocation, threadID); + + if (m->control_pressed) { return userTemplate; } + + for (int i = 0; i < userTemplate.size(); i++) { if (m->control_pressed) { return userTemplate; } databaseLeft->addSequence(*userTemplate[i]); } databaseLeft->generateDB(); - databaseLeft->setNumSeqs(thisTemplate.size()); + databaseLeft->setNumSeqs(userTemplate.size()); } - return thisTemplate; + return userTemplate; } catch(exception& e) { @@ -401,7 +405,6 @@ vector ChimeraSlayer::getTemplate(Sequence* q) { //*************************************************************************************************************** ChimeraSlayer::~ChimeraSlayer() { - delete decalc; if (templateFileName != "self") { if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; } else if (searchMethod == "blast") { delete databaseLeft; } @@ -416,10 +419,10 @@ void ChimeraSlayer::printHeader(ostream& out) { out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; } //*************************************************************************************************************** -Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { +Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc) { try { - Sequence* trim = NULL; - if (trimChimera) { trim = trimQuery; } + Sequence trim; + if (trimChimera) { trim.setName(trimQuery.getName()); trim.setAligned(trimQuery.getAligned()); } if (chimeraFlags == "yes") { string chimeraFlag = "no"; @@ -430,29 +433,135 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { if (chimeraFlag == "yes") { if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) { - m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine(); - outAcc << querySeq->getName() << endl; + m->mothurOut(querySeq.getName() + "\tyes"); m->mothurOutEndLine(); + outAcc << querySeq.getName() << endl; + + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } if (trimChimera) { - int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart]; - int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart]; + int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart; + int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart; - string newAligned = trim->getAligned(); + string newAligned = trim.getAligned(); if (lengthLeft > lengthRight) { //trim right - for (int i = (spotMap[chimeraResults[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } }else { //trim left - for (int i = 0; i < spotMap[chimeraResults[0].winLEnd]; i++) { newAligned[i] = '.'; } + for (int i = 0; i < chimeraResults[0].winLEnd; i++) { newAligned[i] = '.'; } } - trim->setAligned(newAligned); + trim.setAligned(newAligned); } - } } printBlock(chimeraResults[0], chimeraFlag, out); out << endl; - }else { out << querySeq->getName() << "\tno" << endl; } + }else { + out << querySeq.getName() << "\tno" << endl; + } + + return trim; + + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "print"); + exit(1); + } +} +//*************************************************************************************************************** +Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPiece, data_results rightPiece) { + try { + Sequence trim; + + if (trimChimera) { + string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned(); + trim.setName(leftPiece.trimQuery.getName()); trim.setAligned(aligned); + } + + if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) { + + string chimeraFlag = "no"; + if (leftPiece.flag == "yes") { + + if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR) + || + (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + } + + if (rightPiece.flag == "yes") { + if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR) + || + (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + } + + bool rightChimeric = false; + bool leftChimeric = false; + + if (chimeraFlag == "yes") { + //which peice is chimeric or are both + if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } } + if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } } + + if (rightChimeric || leftChimeric) { + m->mothurOut(querySeq.getName() + "\tyes"); m->mothurOutEndLine(); + outAcc << querySeq.getName() << endl; + + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } + + if (trimChimera) { + string newAligned = trim.getAligned(); + + //right side is fine so keep that + if ((leftChimeric) && (!rightChimeric)) { + for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; } + }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that + for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else { //both sides are chimeric, keep longest piece + + int lengthLeftLeft = leftPiece.results[0].winLEnd - leftPiece.results[0].winLStart; + int lengthLeftRight = leftPiece.results[0].winREnd - leftPiece.results[0].winRStart; + + int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4 + int length = lengthLeftLeft; + if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; } + + int lengthRightLeft = rightPiece.results[0].winLEnd - rightPiece.results[0].winLStart; + int lengthRightRight = rightPiece.results[0].winREnd - rightPiece.results[0].winRStart; + + if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; } + if (lengthRightRight > length) { longest = 4; } + + if (longest == 1) { //leftleft + for (int i = (leftPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else if (longest == 2) { //leftright + //get rid of leftleft + for (int i = (leftPiece.results[0].winLStart-1); i < (leftPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; } + //get rid of right + for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else if (longest == 3) { //rightleft + //get rid of left + for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; } + //get rid of rightright + for (int i = (rightPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else { //rightright + //get rid of left + for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; } + //get rid of rightleft + for (int i = (rightPiece.results[0].winLStart-1); i < (rightPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; } + } + } + + trim.setAligned(newAligned); + } + + } + } + + printBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag, out); + out << endl; + }else { + out << querySeq.getName() << "\tno" << endl; + } return trim; @@ -462,17 +571,157 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { exit(1); } } + #ifdef USE_MPI //*************************************************************************************************************** -Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { +Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece, bool& chimFlag) { + try { + MPI_Status status; + bool results = false; + string outAccString = ""; + string outputString = ""; + chimFlag = false; + + Sequence trim; + + if (trimChimera) { + string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned(); + trim.setName(leftPiece.trimQuery.getName()); trim.setAligned(aligned); + } + + + if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) { + + string chimeraFlag = "no"; + if (leftPiece.flag == "yes") { + + if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR) + || + (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + } + + if (rightPiece.flag == "yes") { + if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR) + || + (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + } + + bool rightChimeric = false; + bool leftChimeric = false; + + cout << endl; + + if (chimeraFlag == "yes") { + //which peice is chimeric or are both + if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } } + if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } } + + if (rightChimeric || leftChimeric) { + cout << querySeq.getName() << "\tyes" << endl; + outAccString += querySeq.getName() + "\n"; + results = true; + + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } + + //write to accnos file + int length = outAccString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outAccString.c_str(), length); + + MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status); + chimFlag = true; + delete buf2; + + if (trimChimera) { + string newAligned = trim.getAligned(); + + //right side is fine so keep that + if ((leftChimeric) && (!rightChimeric)) { + for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; } + }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that + for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else { //both sides are chimeric, keep longest piece + + int lengthLeftLeft = leftPiece.results[0].winLEnd - leftPiece.results[0].winLStart; + int lengthLeftRight = leftPiece.results[0].winREnd - leftPiece.results[0].winRStart; + + int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4 + int length = lengthLeftLeft; + if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; } + + int lengthRightLeft = rightPiece.results[0].winLEnd - rightPiece.results[0].winLStart; + int lengthRightRight = rightPiece.results[0].winREnd - rightPiece.results[0].winRStart; + + if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; } + if (lengthRightRight > length) { longest = 4; } + + if (longest == 1) { //leftleft + for (int i = (leftPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else if (longest == 2) { //leftright + //get rid of leftleft + for (int i = (leftPiece.results[0].winLStart-1); i < (leftPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; } + //get rid of right + for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else if (longest == 3) { //rightleft + //get rid of left + for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; } + //get rid of rightright + for (int i = (rightPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + }else { //rightright + //get rid of left + for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; } + //get rid of rightleft + for (int i = (rightPiece.results[0].winLStart-1); i < (rightPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; } + } + } + + trim.setAligned(newAligned); + } + + } + } + + outputString = getBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag); + outputString += "\n"; + + //write to output file + int length = outputString.length(); + char* buf = new char[length]; + memcpy(buf, outputString.c_str(), length); + + MPI_File_write_shared(out, buf, length, MPI_CHAR, &status); + delete buf; + + }else { + outputString += querySeq.getName() + "\tno\n"; + + //write to output file + int length = outputString.length(); + char* buf = new char[length]; + memcpy(buf, outputString.c_str(), length); + + MPI_File_write_shared(out, buf, length, MPI_CHAR, &status); + delete buf; + } + + + return trim; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "print"); + exit(1); + } +} +//*************************************************************************************************************** +Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { try { MPI_Status status; bool results = false; string outAccString = ""; string outputString = ""; - Sequence* trim = NULL; - if (trimChimera) { trim = trimQuery; } + Sequence trim; + if (trimChimera) { trim.setName(trimQuery.getName()); trim.setAligned(trimQuery.getAligned()); } if (chimeraFlags == "yes") { string chimeraFlag = "no"; @@ -483,57 +732,58 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { if (chimeraFlag == "yes") { if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) { - cout << querySeq->getName() << "\tyes" << endl; - outAccString += querySeq->getName() + "\n"; + cout << querySeq.getName() << "\tyes" << endl; + outAccString += querySeq.getName() + "\n"; results = true; + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } + //write to accnos file int length = outAccString.length(); char* buf2 = new char[length]; memcpy(buf2, outAccString.c_str(), length); - + MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status); delete buf2; if (trimChimera) { - int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart]; - int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart]; + int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart; + int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart; - string newAligned = trim->getAligned(); + string newAligned = trim.getAligned(); if (lengthLeft > lengthRight) { //trim right - for (int i = (spotMap[chimeraResults[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } + for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } }else { //trim left - for (int i = 0; i < (spotMap[chimeraResults[0].winLEnd]-1); i++) { newAligned[i] = '.'; } + for (int i = 0; i < (chimeraResults[0].winLEnd-1); i++) { newAligned[i] = '.'; } } - trim->setAligned(newAligned); + trim.setAligned(newAligned); } } } outputString = getBlock(chimeraResults[0], chimeraFlag); outputString += "\n"; - //cout << outputString << endl; + //write to output file int length = outputString.length(); char* buf = new char[length]; memcpy(buf, outputString.c_str(), length); - + MPI_File_write_shared(out, buf, length, MPI_CHAR, &status); delete buf; - + }else { - outputString += querySeq->getName() + "\tno\n"; - //cout << outputString << endl; + outputString += querySeq.getName() + "\tno\n"; + //write to output file int length = outputString.length(); char* buf = new char[length]; memcpy(buf, outputString.c_str(), length); - + MPI_File_write_shared(out, buf, length, MPI_CHAR, &status); delete buf; } - return trim; } catch(exception& e) { @@ -546,27 +796,29 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { //*************************************************************************************************************** int ChimeraSlayer::getChimeras(Sequence* query) { try { - if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned()); } + + trimQuery.setName(query->getName()); trimQuery.setAligned(query->getAligned()); + printResults.trimQuery = trimQuery; chimeraFlags = "no"; - - //filter query - spotMap = runFilter(query); + printResults.flag = "no"; - querySeq = query; + querySeq = *query; //you must create a template vector thisTemplate; - if (templateFileName != "self") { thisTemplate = templateSeqs; } - else { thisTemplate = getTemplate(query); } //fills thistemplate and creates the databases + vector thisFilteredTemplate; + if (templateFileName != "self") { thisTemplate = templateSeqs; thisFilteredTemplate = filteredTemplateSeqs; } + else { thisTemplate = getTemplate(*query, thisFilteredTemplate); } //fills this template and creates the databases if (m->control_pressed) { return 0; } - if (thisTemplate.size() == 0) { return 0; } //not chimeric - //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity - Maligner maligner(thisTemplate, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight); - Slayer slayer(window, increment, minSim, divR, iters, minSNP); + //moved this out of maligner - 4/29/11 + vector refSeqs = getRefSeqs(*query, thisTemplate, thisFilteredTemplate); + + Maligner maligner(refSeqs, match, misMatch, divR, minSim, minCov); + Slayer slayer(window, increment, minSim, divR, iters, minSNP, minBS); if (templateFileName == "self") { if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; } @@ -574,97 +826,104 @@ int ChimeraSlayer::getChimeras(Sequence* query) { } if (m->control_pressed) { return 0; } - - string chimeraFlag = maligner.getResults(query, decalc); + + string chimeraFlag = maligner.getResults(*query, decalc); + if (m->control_pressed) { return 0; } + vector Results = maligner.getOutput(); + + //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } + + if (chimeraFlag == "yes") { - //found in testing realigning only made things worse - if (realign) { - ChimeraReAligner realigner(thisTemplate, match, misMatch); - realigner.reAlign(query, Results); - } + if (realign) { + vector parents; + for (int i = 0; i < Results.size(); i++) { + parents.push_back(Results[i].parentAligned); + } + + ChimeraReAligner realigner; + realigner.reAlign(query, parents); - if (chimeraFlag == "yes") { + } +// cout << query->getAligned() << endl; //get sequence that were given from maligner results - vector seqs; + vector seqs; map removeDups; map::iterator itDup; map parentNameSeq; map::iterator itSeq; for (int j = 0; j < Results.size(); j++) { + 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; +// cout << Results[j].parent << '\t' << Results[j].regionEnd << '\t' << Results[j].regionStart << '\t' << Results[j].regionEnd - Results[j].regionStart +1 << '\t' << Results[j].queryToParentLocal << '\t' << dist << endl; + + + if(Results[j].queryToParentLocal >= 90){ //local match has to be over 90% similarity + + 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; + } + } + } 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); + Sequence seq(itDup->first, itSeq->second); - SeqDist member; + SeqCompare member; member.seq = seq; member.dist = itDup->second; - 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); + sort(seqs.begin(), seqs.end(), compareSeqCompare); //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(); - } + //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); } - //mask then send to slayer... - if (seqMask != "") { - decalc->setMask(seqMask); - - //mask querys - decalc->runMask(query); - - //mask parents - for (int k = 0; k < seqsForSlayer.size(); k++) { - decalc->runMask(seqsForSlayer[k]); - } - - spotMap = decalc->getMaskMap(); +// cout << query->getAligned() << endl; + vector seqsForSlayer; + for (int k = 0; k < seqs.size(); k++) { +// cout << seqs[k].seq->getAligned() << endl; + seqsForSlayer.push_back(seqs[k].seq); +// cout << seqs[k].seq->getName() << endl; } - if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; } - + if (m->control_pressed) { return 0; } + //send to slayer - chimeraFlags = slayer.getResults(query, seqsForSlayer); + chimeraFlags = slayer.getResults(*query, seqsForSlayer); if (m->control_pressed) { return 0; } chimeraResults = slayer.getOutput(); + printResults.flag = chimeraFlags; + printResults.results = chimeraResults; + //free memory - for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } + //for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } } - - //delete maligner; - //delete slayer; - + //cout << endl << endl; return 0; } catch(exception& e) { @@ -675,32 +934,66 @@ int ChimeraSlayer::getChimeras(Sequence* query) { //*************************************************************************************************************** void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){ try { - //out << ":)\n"; - - out << querySeq->getName() << '\t'; + 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 << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t'; + out << flag << '\t' << data.winLStart << "-" << data.winLEnd << '\t' << data.winRStart << "-" << data.winREnd << '\t'; - //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; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "printBlock"); + exit(1); + } +} +//*************************************************************************************************************** +void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag, ostream& out){ + try { + if ((leftChimeric) && (!rightChimeric)) { //print left + out << querySeq.getName() << '\t'; + out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t'; + + out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t'; + out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t'; - //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 << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t'; - //out << "DeltaL: " << (data.qla - data.qlb) << endl; - //out << "DeltaR: " << (data.qra - data.qrb) << endl; - + }else if ((!leftChimeric) && (rightChimeric)) { //print right + out << querySeq.getName() << '\t'; + out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t'; + + out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t'; + out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t'; + + out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t'; + + }else { //print both results + if (leftdata.flag == "yes") { + out << querySeq.getName() + "_LEFT" << '\t'; + out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t'; + + out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t'; + out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t'; + + out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t'; + } + + if (rightdata.flag == "yes") { + if (leftdata.flag == "yes") { out << endl; } + + out << querySeq.getName() + "_RIGHT"<< '\t'; + out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t'; + + out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t'; + out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t'; + + out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t'; + + } + } } catch(exception& e) { m->errorOut(e, "ChimeraSlayer", "printBlock"); @@ -708,18 +1001,74 @@ void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){ } } //*************************************************************************************************************** +string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag){ + try { + + string out = ""; + + if ((leftChimeric) && (!rightChimeric)) { //get left + out += querySeq.getName() + "\t"; + out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t"; + + out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t"; + out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t"; + + out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t"; + + }else if ((!leftChimeric) && (rightChimeric)) { //print right + out += querySeq.getName() + "\t"; + out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t"; + + out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t"; + out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t"; + + out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t"; + + }else { //print both results + + if (leftdata.flag == "yes") { + out += querySeq.getName() + "_LEFT\t"; + out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t"; + + out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t"; + out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t"; + + out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t"; + } + + if (rightdata.flag == "yes") { + if (leftdata.flag == "yes") { out += "\n"; } + out += querySeq.getName() + "_RIGHT\t"; + out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t"; + + out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t"; + out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t"; + + out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t"; + } + } + + return out; + + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "getBlock"); + exit(1); + } +} +//*************************************************************************************************************** string ChimeraSlayer::getBlock(data_struct data, string flag){ try { string outputString = ""; - outputString += querySeq->getName() + "\t"; + outputString += querySeq.getName() + "\t"; outputString += data.parentA.getName() + "\t" + data.parentB.getName() + "\t"; outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t"; outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t"; - outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t"; + outputString += flag + "\t" + toString(data.winLStart) + "-" + toString(data.winLEnd) + "\t" + toString(data.winRStart) + "-" + toString(data.winREnd) + "\t"; return outputString; } @@ -728,5 +1077,215 @@ string ChimeraSlayer::getBlock(data_struct data, string flag){ exit(1); } } +//*************************************************************************************************************** +vector ChimeraSlayer::getRefSeqs(Sequence q, vector& thisTemplate, vector& thisFilteredTemplate){ + try { + + vector refSeqs; + + if (searchMethod == "distance") { + //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate + Sequence* newSeq = new Sequence(q.getName(), q.getAligned()); + runFilter(newSeq); + refSeqs = decalc.findClosest(*newSeq, thisTemplate, thisFilteredTemplate, numWanted, minSim); + delete newSeq; + }else if (searchMethod == "blast") { + refSeqs = getBlastSeqs(q, thisTemplate, numWanted); //fills indexes + }else if (searchMethod == "kmer") { + refSeqs = getKmerSeqs(q, thisTemplate, numWanted); //fills indexes + }else { m->mothurOut("not valid search."); exit(1); } //should never get here + + return refSeqs; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "getRefSeqs"); + exit(1); + } +} //***************************************************************************************************************/ +vector ChimeraSlayer::getBlastSeqs(Sequence q, vector& db, int num) { + try { + + 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 +//cout << "whole length = " << queryUnAligned.length() << '\t' << "left length = " << leftQuery.length() << '\t' << "right length = "<< rightQuery.length() << endl; + Sequence* queryLeft = new Sequence(q.getName(), leftQuery); + Sequence* queryRight = new Sequence(q.getName(), rightQuery); + + vector tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim); + vector tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim); + + + //cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl; +// vector smaller; +// vector larger; +// +// if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; larger = tempIndexesLeft; } +// else { smaller = tempIndexesLeft; larger = tempIndexesRight; } + + //merge results + map seen; + map::iterator it; + vector mergedResults; + + int index = 0; +// for (int i = 0; i < smaller.size(); i++) { + while(index < tempIndexesLeft.size() && index < tempIndexesRight.size()){ + + if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; } + + //add left if you havent already + it = seen.find(tempIndexesLeft[index]); + if (it == seen.end()) { + mergedResults.push_back(tempIndexesLeft[index]); + seen[tempIndexesLeft[index]] = tempIndexesLeft[index]; + } + + //add right if you havent already + it = seen.find(tempIndexesRight[index]); + if (it == seen.end()) { + mergedResults.push_back(tempIndexesRight[index]); + seen[tempIndexesRight[index]] = tempIndexesRight[index]; + } + index++; + } + + + for (int i = index; i < tempIndexesLeft.size(); i++) { + if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; } + + //add right if you havent already + it = seen.find(tempIndexesLeft[i]); + if (it == seen.end()) { + mergedResults.push_back(tempIndexesLeft[i]); + seen[tempIndexesLeft[i]] = tempIndexesLeft[i]; + } + } + + for (int i = index; i < tempIndexesRight.size(); i++) { + if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; } + + //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]; + } + } + //string qname = q->getName().substr(0, q->getName().find_last_of('_')); + //cout << qname << endl; + + if (mergedResults.size() == 0) { numNoParents++; } + + for (int i = 0; i < mergedResults.size(); i++) { + //cout << q->getName() << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl; + if (db[mergedResults[i]]->getName() != q.getName()) { + Sequence temp(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); + refResults.push_back(temp); + } + } + //cout << endl << endl; + + delete queryRight; + delete queryLeft; + + return refResults; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "getBlastSeqs"); + exit(1); + } +} +//*************************************************************************************************************** +vector ChimeraSlayer::getKmerSeqs(Sequence q, vector& db, int num) { + try { + 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(), leftQuery); + Sequence* queryRight = new Sequence(q.getName(), rightQuery); + + vector tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, num); + vector tempIndexesRight = databaseRight->findClosestSequences(queryRight, num); + + //merge results + map seen; + map::iterator it; + vector mergedResults; + + int index = 0; + // for (int i = 0; i < smaller.size(); i++) { + while(index < tempIndexesLeft.size() && index < tempIndexesRight.size()){ + + if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; } + + //add left if you havent already + it = seen.find(tempIndexesLeft[index]); + if (it == seen.end()) { + mergedResults.push_back(tempIndexesLeft[index]); + seen[tempIndexesLeft[index]] = tempIndexesLeft[index]; + } + + //add right if you havent already + it = seen.find(tempIndexesRight[index]); + if (it == seen.end()) { + mergedResults.push_back(tempIndexesRight[index]); + seen[tempIndexesRight[index]] = tempIndexesRight[index]; + } + index++; + } + + + for (int i = index; i < tempIndexesLeft.size(); i++) { + if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; } + + //add right if you havent already + it = seen.find(tempIndexesLeft[i]); + if (it == seen.end()) { + mergedResults.push_back(tempIndexesLeft[i]); + seen[tempIndexesLeft[i]] = tempIndexesLeft[i]; + } + } + + for (int i = index; i < tempIndexesRight.size(); i++) { + if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; } + + //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]; + } + } + + for (int i = 0; i < mergedResults.size(); i++) { + //cout << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl; + if (db[mergedResults[i]]->getName() != q.getName()) { + Sequence temp(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); + refResults.push_back(temp); + + } + } + + //cout << endl; + delete queryRight; + delete queryLeft; + + return refResults; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "getKmerSeqs"); + exit(1); + } +} +//*************************************************************************************************************** +