#include "blastdb.hpp"
//***************************************************************************************************************
-ChimeraSlayer::ChimeraSlayer(string file, string temp, 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() {
+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, string blas, int tid) : Chimera() {
try {
fastafile = file;
templateFileName = temp; templateSeqs = readSeqs(temp);
increment = inc;
numWanted = numw;
realign = r;
+ trimChimera = trim;
+ numNoParents = 0;
+ blastlocation = blas;
+ threadID = tid;
- decalc = new DeCalculator();
-
doPrep();
}
catch(exception& e) {
}
}
//***************************************************************************************************************
-int ChimeraSlayer::doPrep() {
+//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<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, string blas, int tid, bool bg) : Chimera() {
+ try {
+ byGroup = bg;
+ 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;
+
+
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+
+ 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);
+ }
+}
+//***************************************************************************************************************
+//template=self
+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, string blas, int tid) : 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;
+ numNoParents = 0;
+ blastlocation = blas;
+ threadID = tid;
+
- //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++) {
//leftside
kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
ifstream kmerFileTestLeft(kmerDBNameLeft.c_str());
+ bool needToGenerateLeft = true;
- if(!kmerFileTestLeft){
+ if(kmerFileTestLeft){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+ if (GoodFile) { needToGenerateLeft = false; }
+ }
+
+ if(needToGenerateLeft){
for (int i = 0; i < templateSeqs.size(); i++) {
//rightside
kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
ifstream kmerFileTestRight(kmerDBNameRight.c_str());
+ bool needToGenerateRight = true;
+
+ if(kmerFileTestRight){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
+ if (GoodFile) { needToGenerateRight = false; }
+ }
- if(!kmerFileTestRight){
+ if(needToGenerateRight){
for (int i = 0; i < templateSeqs.size(); i++) {
if (m->control_pressed) { return 0; }
}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());
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]); }
+ }
+ }
+
+ //avoids nuisance error from formatdb for making blank blast database
+ if (userTemplate.size() == 0) {
+ return userTemplate;
+ }
+
+ 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, 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(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], out);
+ 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, bool& chimFlag) {
try {
MPI_Status status;
bool results = false;
string outAccString = "";
string outputString = "";
+ chimFlag = false;
- if (chimeraFlags == "yes") {
+ 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( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
- ||
- (chimeraResults[0].bsb >= minBS && chimeraResults[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ 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") {
- if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
- cout << querySeq->getName() << "\tyes" << endl;
- outAccString += querySeq->getName() + "\n";
+ //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(chimeraResults[0]);
+ outputString = getBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag);
outputString += "\n";
- //cout << outputString << endl;
+
//write to output file
int length = outputString.length();
char* buf = new char[length];
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];
}
- return results;
+ 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)
+ ||
+ (chimeraResults[0].bsb >= minBS && chimeraResults[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+
+
+ if (chimeraFlag == "yes") {
+ if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
+ 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";
+
+ //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");
//***************************************************************************************************************
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, ostream& out){
+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 << "yes\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_struct data){
+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 += "yes\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;
+
+ 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<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