if(minDiff > bdiffs) { success = minDiff; } //no good matches
else {
+ if (m->debug) {
+ string fMatches = "";
+ for (int i = 0; i < minFGroup.size(); i++) { for (int j = 0; j < minFGroup[i].size(); j++) { fMatches += toString(minFGroup[i][j]) + " "; } }
+ m->mothurOut("[DEBUG]: forward matches = " + fMatches + "\n");
+ string rMatches = "";
+ for (int i = 0; i < minRGroup.size(); i++) { for (int j = 0; j < minRGroup[i].size(); j++) { rMatches += toString(minRGroup[i][j]) + " "; } }
+ m->mothurOut("[DEBUG]: reverse matches = " + rMatches + "\n");
+ }
bool foundMatch = false;
vector<int> matches;
for (int i = 0; i < minFGroup.size(); i++) {
group = matches[0];
fStart = minFPos[0];
rStart = minRPos[0];
+ if (m->debug) { m->mothurOut("[DEBUG]: found match = " + toString(matches[0]) + ".\n"); }
+ }else {
+ if (m->debug) { m->mothurOut("[DEBUG]: failed too many matches.\n"); }
}
//we have an acceptable match for the forward and reverse, but do they match?
exit(1);
}
+}
+//*******************************************************************/
+int TrimOligos::stripPairedBarcode(Sequence& seq, int& group){
+ try {
+ //look for forward barcode
+ string rawSeq = seq.getUnaligned();
+ int success = bdiffs + 1; //guilty until proven innocent
+ //cout << seq.getName() << endl;
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipbarcodes.begin();it!=ipbarcodes.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+ //cout << it->first << '\t' << foligo << '\t' << roligo << endl;
+ //cout << it->first << '\t' << rawSeq.substr(0,foligo.length()) << '\t' << rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()) << endl;
+ if(rawSeq.length() < foligo.length()){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+ if(rawSeq.length() < roligo.length()){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if (rawSeq.length() < (foligo.length() + roligo.length())) { success = pdiffs + 10; break; }
+
+ if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
+ group = it->first;
+ string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
+ seq.setUnaligned(trimmedSeq.substr(0,(trimmedSeq.length()-roligo.length()))); //trim reverse barcode
+ success = 0;
+ break;
+ }
+ }
+ //cout << "success=" << success << endl;
+ //if you found the barcode or if you don't want to allow for diffs
+ if ((bdiffs == 0) || (success == 0)) { return success; }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ if (ifbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+ vector< vector<int> > minFGroup;
+ vector<int> minFPos;
+
+ //the pair can have duplicates, but we only want to search for the unique forward and reverses, example
+ /*
+ 1 Sarah Westcott
+ 2 John Westcott
+ 3 Anna Westcott
+ 4 Sarah Schloss
+ 5 Pat Schloss
+ 6 Gail Brown
+ 7 Pat Moore
+ only want to look for forward = Sarah, John, Anna, Pat, Gail
+ reverse = Westcott, Schloss, Brown, Moore
+ but if best match forward = 4, and reverse = 1, we want to count as a valid match because forward 1 and forward 4 are the same. so both barcodes map to same group.
+ */
+ //cout << endl << forwardSeq.getName() << endl;
+ for(map<string, vector<int> >::iterator it=ifbarcodes.begin();it!=ifbarcodes.end();it++){
+ string oligo = it->first;
+
+ if(rawSeq.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawSeq.substr(0,oligo.length()+bdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSeq.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }else if(numDiff == minDiff){
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }
+ }
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ string rawRSequence = reverseOligo(seq.getUnaligned());
+ //cout << irbarcodes.size() << '\t' << maxRBarcodeLength << endl;
+ for(map<string, vector<int> >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){
+ string oligo = reverseOligo(it->first);
+ //cout << "r before = " << reverseOligo(oligo) << '\t' << reverseOligo(rawRSequence.substr(0,oligo.length()+bdiffs)) << endl;
+ if(rawRSequence.length() < maxRBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+
+ //cout << "r after = " << reverseOligo(oligo) << '\t' << reverseOligo(temp) << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = rawSeq.length() - minRPos[0];
+ if (fStart > rStart) { foundMatch = false; } //only barcodes not a good sequence
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ string trimmedSeq = rawSeq.substr(0, rStart); //trim reverse barcode
+ seq.setUnaligned(trimmedSeq.substr(fStart)); //trim forward barcode
+ success = minDiff;
+ //cout << "barcode = " << ipbarcodes[group].forward << '\t' << ipbarcodes[group].reverse << endl;
+ }else { success = bdiffs + 100; }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripPairedBarcode");
+ exit(1);
+ }
+
}
//*******************************************************************/
int TrimOligos::stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool keepForward){
}
}
-
+//*******************************************************************/
+int TrimOligos::stripPairedPrimers(Sequence& seq, int& group){
+ try {
+ //look for forward
+ string rawSeq = seq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
+ //cout << seq.getName() << endl;
+ //can you find the forward
+ for(map<int,oligosPair>::iterator it=ipprimers.begin();it!=ipprimers.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ //cout << it->first << '\t' << foligo << '\t' << roligo << endl;
+ //cout << it->first << '\t' << rawSeq.substr(0,foligo.length()) << '\t' << rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()) << endl;
+ if(rawSeq.length() < foligo.length()){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+ if(rawSeq.length() < roligo.length()){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if (rawSeq.length() < (foligo.length() + roligo.length())) { success = pdiffs + 10; break; }
+
+ if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
+ group = it->first;
+ string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
+ seq.setUnaligned(trimmedSeq.substr(0,(trimmedSeq.length()-roligo.length()))); //trim reverse barcode
+ success = 0;
+ break;
+ }
+ }
+ //cout << "success=" << success << endl;
+ //if you found the barcode or if you don't want to allow for diffs
+ if ((pdiffs == 0) || (success == 0)) { return success; }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ if (ifprimers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+ vector< vector<int> > minFGroup;
+ vector<int> minFPos;
+
+ //the pair can have duplicates, but we only want to search for the unique forward and reverses, example
+ /*
+ 1 Sarah Westcott
+ 2 John Westcott
+ 3 Anna Westcott
+ 4 Sarah Schloss
+ 5 Pat Schloss
+ 6 Gail Brown
+ 7 Pat Moore
+ only want to look for forward = Sarah, John, Anna, Pat, Gail
+ reverse = Westcott, Schloss, Brown, Moore
+ but if best match forward = 4, and reverse = 1, we want to count as a valid match because forward 1 and forward 4 are the same. so both barcodes map to same group.
+ */
+ //cout << endl << forwardSeq.getName() << endl;
+ for(map<string, vector<int> >::iterator it=ifprimers.begin();it!=ifprimers.end();it++){
+ string oligo = it->first;
+
+ if(rawSeq.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawSeq.substr(0,oligo.length()+pdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSeq.substr(0,oligo.length()+pdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+
+ if (alnLength == 0) { numDiff = pdiffs + 100; }
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }else if(numDiff == minDiff){
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }
+ }
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irprimers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ string rawRSequence = reverseOligo(seq.getUnaligned());
+
+ for(map<string, vector<int> >::iterator it=irprimers.begin();it!=irprimers.end();it++){
+ string oligo = reverseOligo(it->first);
+ //cout << "r before = " << reverseOligo(oligo) << '\t' << reverseOligo(rawRSequence.substr(0,oligo.length()+pdiffs)) << endl;
+ if(rawRSequence.length() < maxRPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+pdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = pdiffs + 100; }
+
+ //cout << "r after = " << reverseOligo(oligo) << '\t' << reverseOligo(temp) << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = rawSeq.length() - minRPos[0];
+ if (fStart > rStart) { foundMatch = false; } //only primers not a good sequence
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ string trimmedSeq = rawSeq.substr(0, rStart); //trim reverse barcode
+ seq.setUnaligned(trimmedSeq.substr(fStart)); //trim forward barcode
+ success = minDiff;
+ //cout << "primer = " << ipprimers[group].forward << '\t' << ipprimers[group].reverse << endl;
+ }else { success = pdiffs + 100; }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripPairedPrimers");
+ exit(1);
+ }
+
+}
//*******************************************************************/
int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, QualityScores& forwardQual, QualityScores& reverseQual, int& group){
try {
int TrimOligos::stripBarcode(Sequence& seq, int& group){
try {
+ if (paired) { int success = stripPairedBarcode(seq, group); return success; }
+
string rawSequence = seq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
int TrimOligos::stripForward(Sequence& seq, int& group){
try {
+ if (paired) { int success = stripPairedPrimers(seq, group); return success; }
+
string rawSequence = seq.getUnaligned();
int success = pdiffs + 1; //guilty until proven innocent
projects / mothur.git / blobdiff