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++) { if (m->control_pressed) { break; } runFilter(templateSeqs[i]); }
-
-
+ if (searchMethod == "distance") {
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+
+ //run filter on template copying templateSeqs into filteredTemplateSeqs
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
+ runFilter(newSeq);
+ filteredTemplateSeqs.push_back(newSeq);
+ }
+ }
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
if (m->control_pressed) { return 0; }
Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
- filteredTemplateSeqs.push_back(newSeq);
runFilter(newSeq);
+ filteredTemplateSeqs.push_back(newSeq);
}
}
string kmerDBNameLeft;
}else if (searchMethod == "blast") {
//generate blastdb
- databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
+ databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); }
databaseLeft->generateDB();
}else if (searchMethod == "blast") {
//generate blastdb
- databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
+ databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
for (int i = 0; i < userTemplate.size(); i++) { if (m->control_pressed) { return userTemplate; } databaseLeft->addSequence(*userTemplate[i]); }
databaseLeft->generateDB();
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;
+// cout << querySeq->getName() << "\tyes" << endl;
outAccString += querySeq->getName() + "\n";
results = true;
//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 (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) {
- ChimeraReAligner realigner(thisTemplate, match, misMatch);
- realigner.reAlign(query, Results);
+ vector<string> parents;
+ for (int i = 0; i < Results.size(); i++) {
+ parents.push_back(Results[i].parentAligned);
+ }
+
+ ChimeraReAligner realigner;
+ realigner.reAlign(query, parents);
+
}
-
+
//get sequence that were given from maligner results
vector<SeqDist> seqs;
map<string, float> removeDups;
seqs.pop_back();
}
}
-
+
//put seqs into vector to send to slayer
+
+// cout << query->getAligned() << endl;
vector<Sequence*> seqsForSlayer;
- for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); }
+ for (int k = 0; k < seqs.size(); k++) {
+// cout << seqs[k].seq->getAligned() << endl;
+ seqsForSlayer.push_back(seqs[k].seq);
+
+ }
if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; }
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
}
-
+ //cout << endl << endl;
return 0;
}
catch(exception& e) {
//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);
+ 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") {
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);
- Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
- Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
-
- vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
- vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
-
+ 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;
map<int, int>::iterator it;
vector<int> mergedResults;
for (int i = 0; i < smaller.size(); i++) {
+ if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+
//add left if you havent already
it = seen.find(smaller[i]);
if (it == seen.end()) {
}
for (int i = smaller.size(); i < larger.size(); i++) {
+ if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+
//add right if you havent already
it = seen.find(larger[i]);
if (it == seen.end()) {
seen[larger[i]] = larger[i];
}
}
- //numWanted = mergedResults.size();
- //cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted << endl;
for (int i = 0; i < mergedResults.size(); i++) {
- //cout << db[mergedResults[i]]->getName() << '\t' << mergedResults[i] << endl;
-
+ //cout << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl;
if (db[mergedResults[i]]->getName() != q->getName()) {
Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
refResults.push_back(temp);
- //cout << db[mergedResults[i]]->getName() << endl;
+
}
-
- //cout << mergedResults[i] << endl;
}
- //cout << "done " << q->getName() << endl;
+
+
+// for(int i=0;i<refResults.size();i++){
+// cout << refResults[i]->getName() << endl;
+// }
+
delete queryRight;
delete queryLeft;
//***************************************************************************************************************
vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db, int num) {
try {
+ vector<Sequence*> refResults;
//get parts of query
string queryUnAligned = q->getUnaligned();
Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
Sequence* queryRight = new Sequence(q->getName(), rightQuery);
- vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, numWanted);
- vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, numWanted);
+ 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;
for (int i = 0; i < tempIndexesLeft.size(); i++) {
+
+ if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+
//add left if you havent already
it = seen.find(tempIndexesLeft[i]);
if (it == seen.end()) {
//numWanted = mergedResults.size();
//cout << q->getName() << endl;
- vector<Sequence*> refResults;
+
for (int i = 0; i < mergedResults.size(); i++) {
//cout << db[mergedResults[i]]->getName() << endl;
if (db[mergedResults[i]]->getName() != q->getName()) {
projects / mothur.git / blobdiff