#include "blastdb.hpp"
//***************************************************************************************************************
-ChimeraSlayer::ChimeraSlayer(string file, string temp, string mode, int k, int ms, int mms, int win, float div,
+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() {
try {
fastafile = file;
increment = inc;
numWanted = numw;
realign = r;
+ trimChimera = trim;
- decalc = new DeCalculator();
-
doPrep();
}
catch(exception& e) {
}
}
//***************************************************************************************************************
-int ChimeraSlayer::doPrep() {
+ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& 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) : Chimera() {
try {
+ 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;
- //read in all query seqs
- vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
- vector<Sequence*> temp = templateSeqs;
- for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[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");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ChimeraSlayer::doPrep() {
+ try {
+ if (searchMethod == "distance") {
+ //read in all query seqs
+ vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
- createFilter(temp, 0.0); //just removed columns where all seqs have a gap
+ vector<Sequence*> temp = templateSeqs;
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); }
- for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
+ createFilter(temp, 0.0); //just removed columns where all seqs have a gap
- if (m->control_pressed) { return 0; }
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
- //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;
//generate the kmerdb to pass to maligner
if (searchMethod == "kmer") {
- string rightTemplateFileName = "right." + templateFileName;
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
- string leftTemplateFileName = "left." + templateFileName;
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
#ifdef USE_MPI
for (int i = 0; i < templateSeqs.size(); i++) {
bool needToGenerateLeft = true;
if(kmerFileTestLeft){
- bool GoodFile = checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
if (GoodFile) { needToGenerateLeft = false; }
}
bool needToGenerateRight = true;
if(kmerFileTestRight){
- bool GoodFile = checkReleaseVersion(kmerFileTestRight, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
if (GoodFile) { needToGenerateRight = false; }
}
}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);
+
+ if (m->control_pressed) { return 0; }
+
for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); }
databaseLeft->generateDB();
databaseLeft->setNumSeqs(templateSeqs.size());
exit(1);
}
}
+//***************************************************************************************************************
+vector<Sequence*> ChimeraSlayer::getTemplate(Sequence q, vector<Sequence*>& userTemplateFiltered) {
+ try {
+
+ //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<Sequence*> userTemplate;
+
+ 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]); }
+ }
+ }
+
+ string kmerDBNameLeft;
+ string kmerDBNameRight;
+
+ //generate the kmerdb to pass to maligner
+ if (searchMethod == "kmer") {
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
+
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
+#ifdef USE_MPI
+ for (int i = 0; i < userTemplate.size(); i++) {
+
+ if (m->control_pressed) { return userTemplate; }
+
+ string leftFrag = userTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(userTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(userTemplate.size());
+
+ for (int i = 0; i < userTemplate.size(); i++) {
+ if (m->control_pressed) { return userTemplate; }
+
+ string rightFrag = userTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(userTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(userTemplate.size());
+
+#else
+
+
+ for (int i = 0; i < userTemplate.size(); i++) {
+
+ if (m->control_pressed) { return userTemplate; }
+
+ string leftFrag = userTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(userTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(userTemplate.size());
+
+ for (int i = 0; i < userTemplate.size(); i++) {
+ if (m->control_pressed) { return userTemplate; }
+
+ string rightFrag = userTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(userTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(userTemplate.size());
+#endif
+ }else if (searchMethod == "blast") {
+
+ //generate blastdb
+ databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
+
+ 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(userTemplate.size());
+ }
+
+ return userTemplate;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getTemplate");
+ exit(1);
+ }
+}
+
//***************************************************************************************************************
ChimeraSlayer::~ChimeraSlayer() {
- delete decalc;
- if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
- else if (searchMethod == "blast") { delete databaseLeft; }
+ if (templateFileName != "self") {
+ if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
+ else if (searchMethod == "blast") { delete databaseLeft; }
+ }
}
//***************************************************************************************************************
void ChimeraSlayer::printHeader(ostream& out) {
out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
}
//***************************************************************************************************************
-int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
+Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc) {
try {
+ Sequence trim;
+ if (trimChimera) { trim.setName(trimQuery.getName()); trim.setAligned(trimQuery.getAligned()); }
+
if (chimeraFlags == "yes") {
string chimeraFlag = "no";
if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
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 = chimeraResults[0].winLEnd - chimeraResults[0].winLStart;
+ int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart;
+
+ string newAligned = trim.getAligned();
+
+ if (lengthLeft > lengthRight) { //trim right
+ for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //trim left
+ for (int i = 0; i < chimeraResults[0].winLEnd; i++) { newAligned[i] = '.'; }
+ }
+ trim.setAligned(newAligned);
+ }
}
}
printBlock(chimeraResults[0], chimeraFlag, out);
out << endl;
- }else { out << querySeq->getName() << "\tno" << endl; }
+ }else {
+ out << querySeq.getName() << "\tno" << endl;
+ }
- return 0;
+ return trim;
}
catch(exception& e) {
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;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+
#ifdef USE_MPI
//***************************************************************************************************************
-int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
+Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece) {
+ try {
+ MPI_Status status;
+ bool results = false;
+ string outAccString = "";
+ string outputString = "";
+
+ 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);
+ 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;
+ if (trimChimera) { trim.setName(trimQuery.getName()); trim.setAligned(trimQuery.getAligned()); }
+
if (chimeraFlags == "yes") {
string chimeraFlag = "no";
if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
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 = chimeraResults[0].winLEnd - chimeraResults[0].winLStart;
+ int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart;
+
+ string newAligned = trim.getAligned();
+ if (lengthLeft > lengthRight) { //trim right
+ for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //trim left
+ for (int i = 0; i < (chimeraResults[0].winLEnd-1); i++) { newAligned[i] = '.'; }
+ }
+ 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 results;
+ return trim;
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayer", "print");
//***************************************************************************************************************
int ChimeraSlayer::getChimeras(Sequence* query) {
try {
+
+ 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;
- //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
- maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
- slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
-
- if (m->control_pressed) { return 0; }
+ //you must create a template
+ vector<Sequence*> thisTemplate;
+ vector<Sequence*> thisFilteredTemplate;
+ if (templateFileName != "self") { thisTemplate = templateSeqs; thisFilteredTemplate = filteredTemplateSeqs; }
+ else { thisTemplate = getTemplate(*query, thisFilteredTemplate); } //fills this template and creates the databases
- string chimeraFlag = maligner->getResults(query, decalc);
if (m->control_pressed) { return 0; }
- vector<results> Results = maligner->getOutput();
-
- //found in testing realigning only made things worse
- if (realign) {
- ChimeraReAligner realigner(templateSeqs, match, misMatch);
- realigner.reAlign(query, Results);
+
+ if (thisTemplate.size() == 0) { return 0; } //not chimeric
+
+ //moved this out of maligner - 4/29/11
+ vector<Sequence> 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; }
+ else if (searchMethod == "blast") { delete databaseLeft; }
}
+
+ if (m->control_pressed) { return 0; }
+
+ string chimeraFlag = maligner.getResults(*query, decalc);
+ if (m->control_pressed) { return 0; }
+
+ vector<results> Results = maligner.getOutput();
+
+ //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
+
if (chimeraFlag == "yes") {
+ if (realign) {
+ vector<string> parents;
+ for (int i = 0; i < Results.size(); i++) {
+ parents.push_back(Results[i].parentAligned);
+ }
+
+ ChimeraReAligner realigner;
+ realigner.reAlign(query, parents);
+
+ }
+
+// cout << query->getAligned() << endl;
//get sequence that were given from maligner results
- vector<SeqDist> seqs;
+ vector<SeqCompare> seqs;
map<string, float> removeDups;
map<string, float>::iterator itDup;
map<string, string> parentNameSeq;
map<string, string>::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<Sequence*> 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<Sequence> 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();
+ 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) {
//***************************************************************************************************************
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");
}
}
//***************************************************************************************************************
+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;
}
exit(1);
}
}
+//***************************************************************************************************************
+vector<Sequence> ChimeraSlayer::getRefSeqs(Sequence q, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate){
+ try {
+
+ vector<Sequence> 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<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db, int num) {
+ try {
+
+ vector<Sequence> 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<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim);
+ vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim);
+
+
+ //cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl;
+// vector<int> smaller;
+// vector<int> larger;
+//
+// if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; larger = tempIndexesLeft; }
+// else { smaller = tempIndexesLeft; larger = tempIndexesRight; }
+
+ //merge results
+ map<int, int> seen;
+ map<int, int>::iterator it;
+ vector<int> 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;
+
+ 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;
+
+ if (refResults.size() == 0) { m->mothurOut("[WARNING]: megablast returned 0 potential parents, so we are not able to check " + q.getName() + ". This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+
+ return refResults;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getBlastSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<Sequence> ChimeraSlayer::getKmerSeqs(Sequence q, vector<Sequence*>& db, int num) {
+ try {
+ vector<Sequence> 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<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, num);
+ vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, num);
+
+ //merge results
+ map<int, int> seen;
+ map<int, int>::iterator it;
+ vector<int> 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);
+ }
+}
+//***************************************************************************************************************
+
projects / mothur.git / blobdiff