#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();
exit(1);
}
}
+//***************************************************************************************************************
+ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string name, string mode, string abunds, int k, int ms, int mms, int win, float div,
+ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() {
+ 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;
+ includeAbunds = abunds;
+ trimChimera = trim;
+
+ //read name file and create nameMapRank
+ readNameFile(name);
+
+ decalc = new DeCalculator();
+
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+
+ //run filter on template
+ for (int i = 0; i < templateSeqs.size(); i++) { runFilter(templateSeqs[i]); }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ChimeraSlayer::readNameFile(string name) {
+ try {
+ ifstream in;
+ m->openInputFile(name, in);
+
+ int maxRank = 0;
+ int minRank = 10000000;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ string thisname, repnames;
+
+ in >> thisname; m->gobble(in); //read from first column
+ in >> repnames; //read from second column
+
+ map<string, vector<string> >::iterator it = nameMapRank.find(thisname);
+ if (it == nameMapRank.end()) {
+
+ vector<string> splitRepNames;
+ m->splitAtComma(repnames, splitRepNames);
+
+ nameMapRank[thisname] = splitRepNames;
+
+ if (splitRepNames.size() > maxRank) { maxRank = splitRepNames.size(); }
+ if (splitRepNames.size() < minRank) { minRank = splitRepNames.size(); }
+
+ }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ //sanity check to make sure files match
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ map<string, vector<string> >::iterator it = nameMapRank.find(templateSeqs[i]->getName());
+
+ if (it == nameMapRank.end()) { m->mothurOut("[ERROR]: " + templateSeqs[i]->getName() + " is not in namesfile, but is in fastafile. Every name in fasta file must be in first column of names file."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+
+ if (maxRank == minRank) { m->mothurOut("[ERROR]: all sequences in namesfile have the same abundance, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "readNameFile");
+ exit(1);
+ }
+}
+
//***************************************************************************************************************
int ChimeraSlayer::doPrep() {
try {
//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(-1.0, -1.0, 1, -3);
+
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) {
+ try {
+
+ vector<Sequence*> thisTemplate;
+
+ int thisRank;
+ string thisName = q->getName();
+ map<string, vector<string> >::iterator itRank = nameMapRank.find(thisName); // you will find it because we already sanity checked
+ thisRank = (itRank->second).size();
+
+ //create list of names we want to put into the template
+ set<string> namesToAdd;
+ for (itRank = nameMapRank.begin(); itRank != nameMapRank.end(); itRank++) {
+ if (itRank->first != thisName) {
+ if (includeAbunds == "greaterequal") {
+ if ((itRank->second).size() >= thisRank) {
+ //you are more abundant than me or equal to my abundance
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
+ }else if (includeAbunds == "greater") {
+ if ((itRank->second).size() > thisRank) {
+ //you are more abundant than me
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
+ }else if (includeAbunds == "all") {
+ //add everyone
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
+ }
+ }
+
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (namesToAdd.count(templateSeqs[i]->getName()) != 0) {
+ thisTemplate.push_back(templateSeqs[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 < thisTemplate.size(); i++) {
+
+ if (m->control_pressed) { return thisTemplate; }
+
+ string leftFrag = thisTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(thisTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+ if (m->control_pressed) { return thisTemplate; }
+
+ string rightFrag = thisTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(thisTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(thisTemplate.size());
+
+#else
+
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+
+ if (m->control_pressed) { return thisTemplate; }
+
+ string leftFrag = thisTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(thisTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+ if (m->control_pressed) { return thisTemplate; }
+
+ string rightFrag = thisTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(thisTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(thisTemplate.size());
+#endif
+ }else if (searchMethod == "blast") {
+
+ //generate blastdb
+ databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
+
+ for (int i = 0; i < thisTemplate.size(); i++) { if (m->control_pressed) { return thisTemplate; } databaseLeft->addSequence(*thisTemplate[i]); }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+ }
+
+ return thisTemplate;
+
+ }
+ 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 = NULL;
+ if (trimChimera) { trim = trimQuery; }
+
if (chimeraFlags == "yes") {
string chimeraFlag = "no";
if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
outAcc << querySeq->getName() << endl;
+
+ if (trimChimera) {
+ int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart];
+ int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart];
+
+ string newAligned = trim->getAligned();
+
+ if (lengthLeft > lengthRight) { //trim right
+ for (int i = (spotMap[chimeraResults[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //trim left
+ for (int i = 0; i < spotMap[chimeraResults[0].winLEnd]; i++) { newAligned[i] = '.'; }
+ }
+ trim->setAligned(newAligned);
+ }
+
}
}
out << 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 = NULL;
+
+ if (trimChimera) {
+ string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
+ trim = new Sequence(leftPiece.trimQuery.getName(), 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 (trimChimera) {
+ string newAligned = trim->getAligned();
+
+ //right side is fine so keep that
+ if ((leftChimeric) && (!rightChimeric)) {
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //both sides are chimeric, keep longest piece
+
+ int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLEnd] - leftPiece.spotMap[leftPiece.results[0].winLStart];
+ int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winREnd] - leftPiece.spotMap[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.spotMap[rightPiece.results[0].winLEnd] - rightPiece.spotMap[rightPiece.results[0].winLStart];
+ int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winREnd] - rightPiece.spotMap[rightPiece.results[0].winRStart];
+
+ if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
+ if (lengthRightRight > length) { longest = 4; }
+
+ if (longest == 1) { //leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 2) { //leftright
+ //get rid of leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winLStart]-1); i < (leftPiece.spotMap[leftPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ //get rid of right
+ for (int i = (rightPiece.spotMap[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.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightright
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //rightright
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightleft
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < (rightPiece.spotMap[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 = NULL;
+
+ if (trimChimera) {
+ string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
+ trim = new Sequence(leftPiece.trimQuery.getName(), 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) {
+ cout << querySeq->getName() << "\tyes" << endl;
+ outAccString += querySeq->getName() + "\n";
+ results = true;
+
+ //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.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //both sides are chimeric, keep longest piece
+
+ int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLEnd] - leftPiece.spotMap[leftPiece.results[0].winLStart];
+ int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winREnd] - leftPiece.spotMap[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.spotMap[rightPiece.results[0].winLEnd] - rightPiece.spotMap[rightPiece.results[0].winLStart];
+ int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winREnd] - rightPiece.spotMap[rightPiece.results[0].winRStart];
+
+ if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
+ if (lengthRightRight > length) { longest = 4; }
+
+ if (longest == 1) { //leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 2) { //leftright
+ //get rid of leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winLStart]-1); i < (leftPiece.spotMap[leftPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ //get rid of right
+ for (int i = (rightPiece.spotMap[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.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightright
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //rightright
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightleft
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < (rightPiece.spotMap[rightPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ }
+
+ trim->setAligned(newAligned);
+ }
+
+ }
+ }
+
+ outputString = getBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag);
+ outputString += "\n";
+
+ //write to output file
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+ delete buf;
+
+ }else {
+ outputString += querySeq->getName() + "\tno\n";
+
+ //write to output file
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+ delete buf;
+ }
+
+
+ return trim;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
try {
MPI_Status status;
bool results = false;
string outAccString = "";
string outputString = "";
+ Sequence* trim = NULL;
+ if (trimChimera) { trim = trimQuery; }
+
if (chimeraFlags == "yes") {
string chimeraFlag = "no";
if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
int length = outAccString.length();
char* buf2 = new char[length];
memcpy(buf2, outAccString.c_str(), length);
-
+
MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
delete buf2;
+
+ if (trimChimera) {
+ int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart];
+ int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart];
+
+ string newAligned = trim->getAligned();
+ if (lengthLeft > lengthRight) { //trim right
+ for (int i = (spotMap[chimeraResults[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //trim left
+ for (int i = 0; i < (spotMap[chimeraResults[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ 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;
+
//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 {
+ if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned()); printResults.trimQuery = *trimQuery; }
+
chimeraFlags = "no";
+ printResults.flag = "no";
//filter query
spotMap = runFilter(query);
+ printResults.spotMap = spotMap;
querySeq = query;
+ //you must create a template
+ vector<Sequence*> thisTemplate;
+ if (templateFileName != "self") { thisTemplate = templateSeqs; }
+ else { thisTemplate = getTemplate(query); } //fills thistemplate and creates the databases
+
+ if (m->control_pressed) { return 0; }
+
+ if (thisTemplate.size() == 0) { return 0; } //not chimeric
+
//referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
- maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
- slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
+ Maligner maligner(thisTemplate, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
+ Slayer slayer(window, increment, minSim, divR, iters, minSNP);
+
+ 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);
+
+ string chimeraFlag = maligner.getResults(query, decalc);
if (m->control_pressed) { return 0; }
- vector<results> Results = maligner->getOutput();
-
+ vector<results> Results = maligner.getOutput();
+
//found in testing realigning only made things worse
if (realign) {
- ChimeraReAligner realigner(templateSeqs, match, misMatch);
+ ChimeraReAligner realigner(thisTemplate, match, misMatch);
realigner.reAlign(query, Results);
}
}
for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
- //Sequence* seq = getSequence(itDup->first); //makes copy so you can filter and mask and not effect template
itSeq = parentNameSeq.find(itDup->first);
-//cout << itDup->first << itSeq->second << endl;
Sequence* seq = new Sequence(itDup->first, itSeq->second);
SeqDist member;
//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 (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; }
-
+
//send to slayer
- chimeraFlags = slayer->getResults(query, seqsForSlayer);
+ chimeraFlags = slayer.getResults(query, seqsForSlayer);
if (m->control_pressed) { return 0; }
- chimeraResults = slayer->getOutput();
+ chimeraResults = slayer.getOutput();
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
+
+ printResults.spotMap = spotMap;
+ printResults.flag = chimeraFlags;
+ printResults.results = chimeraResults;
}
- delete maligner;
- delete slayer;
-
return 0;
}
catch(exception& e) {
//***************************************************************************************************************
void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
try {
- //out << ":)\n";
-
out << querySeq->getName() << '\t';
out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t';
- //out << "Left Window: " << spotMap[data.winLStart] << " " << spotMap[data.winLEnd] << endl;
- //out << "Right Window: " << spotMap[data.winRStart] << " " << spotMap[data.winREnd] << endl;
-
+
out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[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.spotMap[leftdata.results[0].winLStart] << "-" << leftdata.spotMap[leftdata.results[0].winLEnd] << '\t' << leftdata.spotMap[leftdata.results[0].winRStart] << "-" << leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart] << "-" << rightdata.spotMap[rightdata.results[0].winLEnd] << '\t' << rightdata.spotMap[rightdata.results[0].winRStart] << "-" << rightdata.spotMap[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.spotMap[leftdata.results[0].winLStart] << "-" << leftdata.spotMap[leftdata.results[0].winLEnd] << '\t' << leftdata.spotMap[leftdata.results[0].winRStart] << "-" << leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart] << "-" << rightdata.spotMap[rightdata.results[0].winLEnd] << '\t' << rightdata.spotMap[rightdata.results[0].winRStart] << "-" << rightdata.spotMap[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.spotMap[leftdata.results[0].winLStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winLEnd]) + "\t" + toString(leftdata.spotMap[leftdata.results[0].winRStart]) + "-" + toString(leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winLEnd]) + "\t" + toString(rightdata.spotMap[rightdata.results[0].winRStart]) + "-" + toString(rightdata.spotMap[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.spotMap[leftdata.results[0].winLStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winLEnd]) + "\t" + toString(leftdata.spotMap[leftdata.results[0].winRStart]) + "-" + toString(leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winLEnd]) + "\t" + toString(rightdata.spotMap[rightdata.results[0].winRStart]) + "-" + toString(rightdata.spotMap[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 {
projects / mothur.git / blobdiff