TrimOligos::TrimOligos(int p, int b, int l, int s, map<string, int> pr, map<string, int> br, vector<string> r, vector<string> lk, vector<string> sp){
try {
m = MothurOut::getInstance();
+ paired = false;
+ trashCode = "";
pdiffs = p;
bdiffs = b;
revPrimer = r;
linker = lk;
spacer = sp;
+ maxFBarcodeLength = 0;
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ if(it->first.length() > maxFBarcodeLength){
+ maxFBarcodeLength = it->first.length();
+ }
+ }
+ maxFPrimerLength = 0;
+ map<string,int>::iterator it;
+ for(it=primers.begin();it!=primers.end();it++){
+ if(it->first.length() > maxFPrimerLength){
+ maxFPrimerLength = it->first.length();
+ }
+ }
+
+ maxLinkerLength = 0;
+ for(int i = 0; i < linker.size(); i++){
+ if(linker[i].length() > maxLinkerLength){
+ maxLinkerLength = linker[i].length();
+ }
+ }
+
+ maxSpacerLength = 0;
+ for(int i = 0; i < spacer.size(); i++){
+ if(spacer[i].length() > maxSpacerLength){
+ maxSpacerLength = spacer[i].length();
+ }
+ }
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "TrimOligos");
}
/********************************************************************/
//strip, pdiffs, bdiffs, primers, barcodes, revPrimers
-TrimOligos::TrimOligos(int p, int b, int l, int s, map<int, oligosPair> pr, map<int, oligosPair> br, vector<string> lk, vector<string> sp){
+TrimOligos::TrimOligos(int p, int b, int l, int s, map<int, oligosPair> pr, map<int, oligosPair> br){
try {
m = MothurOut::getInstance();
bdiffs = b;
ldiffs = l;
sdiffs = s;
+ paired = true;
+ trashCode = "";
- ibarcodes = br;
- iprimers = pr;
- linker = lk;
- spacer = sp;
+ maxFBarcodeLength = 0;
+ for(map<int,oligosPair>::iterator it=br.begin();it!=br.end();it++){
+ string forward = it->second.forward;
+ map<string, vector<int> >::iterator itForward = ifbarcodes.find(forward);
+
+ if(forward.length() > maxFBarcodeLength){ maxFBarcodeLength = forward.length(); }
+
+ if (itForward == ifbarcodes.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ ifbarcodes[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ maxFPrimerLength = 0;
+ for(map<int,oligosPair>::iterator it=pr.begin();it!=pr.end();it++){
+ string forward = it->second.forward;
+ map<string, vector<int> >::iterator itForward = ifprimers.find(forward);
+
+ if(forward.length() > maxFPrimerLength){ maxFPrimerLength = forward.length(); }
+
+ if (itForward == ifprimers.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ ifprimers[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ maxRBarcodeLength = 0;
+ for(map<int,oligosPair>::iterator it=br.begin();it!=br.end();it++){
+ string forward = it->second.reverse;
+ map<string, vector<int> >::iterator itForward = irbarcodes.find(forward);
+
+ if(forward.length() > maxRBarcodeLength){ maxRBarcodeLength = forward.length(); }
+
+ if (itForward == irbarcodes.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ irbarcodes[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ maxRPrimerLength = 0;
+ for(map<int,oligosPair>::iterator it=pr.begin();it!=pr.end();it++){
+ string forward = it->second.reverse;
+ map<string, vector<int> >::iterator itForward = irprimers.find(forward);
+
+ if(forward.length() > maxRPrimerLength){ maxRPrimerLength = forward.length(); }
+
+ if (itForward == irprimers.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ irprimers[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ ipbarcodes = br;
+ ipprimers = pr;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "TrimOligos");
barcodes = br;
primers = pr;
revPrimer = r;
+ paired = false;
+ trashCode = "";
+
+ maxFBarcodeLength = 0;
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+ if(oligo.length() > maxFBarcodeLength){
+ maxFBarcodeLength = oligo.length();
+ }
+ }
+ maxRBarcodeLength = maxFBarcodeLength;
+
+ maxFPrimerLength = 0;
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+ if(oligo.length() > maxFPrimerLength){
+ maxFPrimerLength = oligo.length();
+ }
+ }
+ maxRPrimerLength = maxFPrimerLength;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "TrimOligos");
}
/********************************************************************/
TrimOligos::~TrimOligos() {}
+//********************************************************************/
+bool TrimOligos::findForward(Sequence& seq, int& primerStart, int& primerEnd){
+ try {
+
+ string rawSequence = seq.getUnaligned();
+ trashCode = "";
+
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+
+ if(rawSequence.length() < oligo.length()) { break; }
+
+ //search for primer
+ int olength = oligo.length();
+ for (int j = 0; j < rawSequence.length()-olength; j++){
+ if (m->control_pressed) { primerStart = 0; primerEnd = 0; return false; }
+ string rawChunk = rawSequence.substr(j, olength);
+ if(compareDNASeq(oligo, rawChunk)) {
+ primerStart = j;
+ primerEnd = primerStart + olength;
+ return true;
+ }
+
+ }
+ }
+
+ primerStart = 0; primerEnd = 0;
+ //if you don't want to allow for diffs
+ if (pdiffs == 0) { trashCode = "f"; return false; }
+ else { //try aligning and see if you can find it
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+
+ Alignment* alignment;
+ if (primers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+
+ string prim = it->first;
+ //search for primer
+ int olength = prim.length();
+ if (rawSequence.length() < olength) {} //ignore primers too long for this seq
+ else{
+ for (int j = 0; j < rawSequence.length()-olength; j++){
+
+ string oligo = it->first;
+
+ if (m->control_pressed) { primerStart = 0; primerEnd = 0; return false; }
+
+ string rawChunk = rawSequence.substr(j, olength+pdiffs);
+
+ //use needleman to align first primer.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawChunk);
+ 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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ primerStart = j;
+ primerEnd = primerStart + alnLength;
+ }else if(numDiff == minDiff){ minCount++; }
+ }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ if(minDiff > pdiffs) { primerStart = 0; primerEnd = 0; trashCode = "f"; return false; } //no good matches
+ else if(minCount > 1) { primerStart = 0; primerEnd = 0; trashCode = "f"; return false; } //can't tell the difference between multiple primers
+ else{ trashCode = ""; return true; }
+ }
+
+ trashCode = "f";
+ primerStart = 0; primerEnd = 0;
+ return false;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripForward");
+ exit(1);
+ }
+}
+//******************************************************************/
+bool TrimOligos::findReverse(Sequence& seq, int& primerStart, int& primerEnd){
+ try {
+ trashCode = "";
+ string rawSequence = seq.getUnaligned();
+
+ for(int i=0;i<revPrimer.size();i++){
+ string oligo = revPrimer[i];
+ if(rawSequence.length() < oligo.length()) { break; }
+
+ //search for primer
+ int olength = oligo.length();
+ for (int j = rawSequence.length()-olength; j >= 0; j--){
+ if (m->control_pressed) { primerStart = 0; primerEnd = 0; return false; }
+ string rawChunk = rawSequence.substr(j, olength);
+
+ if(compareDNASeq(oligo, rawChunk)) {
+ primerStart = j;
+ primerEnd = primerStart + olength;
+ return true;
+ }
+
+ }
+ }
+
+ trashCode = "r";
+ primerStart = 0; primerEnd = 0;
+ return false;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PcrSeqsCommand", "findReverse");
+ exit(1);
+ }
+}
//*******************************************************************/
+
int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
try {
-
+ trashCode = "";
+ if (paired) { int success = stripPairedBarcode(seq, qual, group); return success; }
+
string rawSequence = seq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
}
success = 0;
- break;
+ trashCode = "";
+ return success;
}
}
//if you found the barcode or if you don't want to allow for diffs
- if ((bdiffs == 0) || (success == 0)) { return success; }
+ if (bdiffs == 0) { trashCode = "b"; return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (barcodes.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=barcodes.begin();it!=barcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
+ if (barcodes.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;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
- success = bdiffs + 10;
+ if(rawSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; trashCode = "b";
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
}
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
+ if(minDiff > bdiffs) { trashCode = "b"; success = minDiff; } //no good matches
+ else if(minCount > 1) { trashCode = "b"; success = bdiffs + 100; } //can't tell the difference between multiple barcodes
else{ //use the best match
group = minGroup;
seq.setUnaligned(rawSequence.substr(minPos));
qual.trimQScores(minPos, -1);
}
success = minDiff;
+ trashCode = "";
}
if (alignment != NULL) { delete alignment; }
}
}
//*******************************************************************/
-int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, QualityScores& forwardQual, QualityScores& reverseQual, int& group){
+int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& group){
try {
+ trashCode = "";
//look for forward barcode
string rawFSequence = forwardSeq.getUnaligned();
string rawRSequence = reverseSeq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
//can you find the forward barcode
- for(map<int,oligosPair>::iterator it=ibarcodes.begin();it!=ibarcodes.end();it++){
+ for(map<int,oligosPair>::iterator it=ipbarcodes.begin();it!=ipbarcodes.end();it++){
string foligo = it->second.forward;
string roligo = it->second.reverse;
if(rawFSequence.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;
+ trashCode += "b";
+ break;
}
if(rawRSequence.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
+ trashCode += "d";
break;
}
- if((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
- group = it->first;
- forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
- reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
- forwardQual.trimQScores(foligo.length(), -1);
- reverseQual.trimQScores(-1, rawRSequence.length()-roligo.length());
- success = 0;
- break;
- }
+ if(compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) {
+ if (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length()))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ success = 0; trashCode = "";
+ return success;
+ }
+ }else {
+ trashCode = "b";
+ if (!compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length()))) { trashCode += "d"; }
+ }
}
//if you found the barcode or if you don't want to allow for diffs
- if ((bdiffs == 0) || (success == 0)) { return success; }
+ if (bdiffs == 0) { return success; }
else { //try aligning and see if you can find it
-
- //look for forward
- int maxLength = 0;
-
+ trashCode = "";
Alignment* alignment;
- if (ibarcodes.size() > 0) {
- for(map<int,oligosPair>::iterator it=ibarcodes.begin();it!=ibarcodes.end();it++){
- if(it->second.forward.length() > maxLength){ maxLength = it->second.forward.length(); }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
- }else{ alignment = NULL; }
+ 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;
- int minFGroup = -1;
- int minFPos = 0;
-
- for(map<int,oligosPair>::iterator it=ibarcodes.begin();it!=ibarcodes.end();it++){
- string oligo = it->second.forward;
+ 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(rawFSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawFSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
success = bdiffs + 10;
break;
}
-
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+bdiffs) << endl;
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawFSequence.substr(0,oligo.length()+bdiffs));
+ alignment->alignPrimer(oligo, rawFSequence.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; } }
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 = it->first;
- minFPos = 0;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
- minFPos++;
+ tempminFPos++;
}
}
+ minFPos.push_back(tempminFPos);
}else if(numDiff == minDiff){
- minCount++;
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
}
-
}
-
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > bdiffs) { trashCode = "b"; minFGroup.clear(); success = minDiff; } //no good matches
+ //else{
//check for reverse match
if (alignment != NULL) { delete alignment; }
- maxLength = 0;
- if (ibarcodes.size() > 0) {
- for(map<int,oligosPair>::iterator it=ibarcodes.begin();it!=ibarcodes.end();it++){
- if(it->second.reverse.length() > maxLength){ maxLength = it->second.reverse.length(); }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
- }else{ alignment = NULL; }
+ 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;
- int minRGroup = -1;
- int minRPos = 0;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
- for(map<int,oligosPair>::iterator it=ibarcodes.begin();it!=ibarcodes.end();it++){
- string oligo = it->second.reverse;
-
- if(rawRSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ for(map<string, vector<int> >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << 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->align(oligo, rawRSequence.substr((rawRSequence.length()-(oligo.length()+bdiffs)),oligo.length()+bdiffs));
+ alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
int alnLength = oligo.length();
- for(int i=0;i<alnLength;i++){ if(oligo[i] != '-'){ alnLength = i; break; } }
+ 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;
- minRGroup = it->first;
- minRPos = 0;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
- minRPos++;
+ tempminRPos++;
}
}
+ minRPos.push_back(tempminRPos);
}else if(numDiff == minDiff){
- minCount++;
+ 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 if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > bdiffs) { trashCode += "d"; 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 = minRPos[0];
+ }
+
//we have an acceptable match for the forward and reverse, but do they match?
- if (minFGroup == minRGroup) {
- group = minFGroup;
- forwardSeq.setUnaligned(rawFSequence.substr(minFPos));
- reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-minRPos)));
- forwardQual.trimQScores(minFPos, -1);
- reverseQual.trimQScores(-1, rawRSequence.length()-minRPos);
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
success = minDiff;
- }else { success = bdiffs + 100; }
+ }else { if (trashCode == "") { trashCode = "bd"; } success = bdiffs + 100; }
}
- }
+ //}
if (alignment != NULL) { delete alignment; }
}
+ //catchall for case I didn't think of
+ if ((trashCode == "") && (success > bdiffs)) { trashCode = "bd"; }
+
return success;
}
}
//*******************************************************************/
-int TrimOligos::stripBarcode(Sequence& seq, int& group){
+int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, QualityScores& forwardQual, QualityScores& reverseQual, int& group){
try {
-
- string rawSequence = seq.getUnaligned();
+ trashCode = "";
+
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
- //can you find the barcode
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
+ //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;
+
+ if(rawFSequence.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
+ trashCode = "b";
+ break;
+ }
+ if(rawRSequence.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
+ trashCode += "d";
break;
}
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
-
- success = 0;
- break;
+ if(compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) {
+ if (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length()))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ forwardQual.trimQScores(foligo.length(), -1);
+ reverseQual.trimQScores(-1, rawRSequence.length()-roligo.length());
+ success = 0; trashCode = "";
+ return success;
+ }
+ }else {
+ trashCode = "b";
+ if (!compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length()))) { trashCode += "d";
+ }
}
}
//if you found the barcode or if you don't want to allow for diffs
- if ((bdiffs == 0) || (success == 0)) { return success; }
-
+ if (bdiffs == 0) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
+ trashCode = "";
Alignment* alignment;
- if (barcodes.size() > 0) {
- map<string,int>::iterator it=barcodes.begin();
-
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
+ 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;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ 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;
- // int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawFSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
success = bdiffs + 10;
break;
}
-
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+bdiffs) << endl;
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
+ alignment->alignPrimer(oligo, rawFSequence.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; }
- }
+ 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);
+ 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;
- minGroup = it->second;
- minPos = 0;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
- minPos++;
+ 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);
}
- else if(numDiff == minDiff){
- minCount++;
- }
-
}
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > bdiffs) { trashCode = "b"; minFGroup.clear(); 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;
+
+ for(map<string, vector<int> >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << 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 << "after = " << oligo << '\t' << 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);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > bdiffs) { trashCode = "d"; 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 = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ forwardQual.trimQScores(fStart, -1);
+ reverseQual.trimQScores(rStart, -1);
+ success = minDiff;
+ }else { if (trashCode == "") { trashCode = "bd"; } success = bdiffs + 100; }
+ }
+ //}
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(minPos));
- success = minDiff;
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ //catchall for case I didn't think of
+ if ((trashCode == "") && (success > bdiffs)) { trashCode = "bd"; }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripIBarcode");
+ exit(1);
+ }
+
+}
+//*******************************************************************/
+int TrimOligos::stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group){
+ try {
+ trashCode = "";
+
+ //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
+ trashCode = "b";
+ 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
+ trashCode += "d";
+ break;
+ }
+
+ if(compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) { //find forward
+ if (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()))) { //find reverse
+ group = it->first;
+ string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
+ seq.setUnaligned(trimmedSeq.substr(0,(trimmedSeq.length()-roligo.length()))); //trim reverse barcode
+ if(qual.getName() != ""){
+ qual.trimQScores(-1, rawSeq.length()-roligo.length());
+ qual.trimQScores(foligo.length(), -1);
+ }
+ success = 0;
+ trashCode = "";
+ return success;
+ }
+ }else {
+ trashCode = "b";
+ if (!compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()))) { trashCode += "d"; }
+ }
+ }
+ //cout << "success=" << success << endl;
+ //if you found the barcode or if you don't want to allow for diffs
+ if (bdiffs == 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) { trashCode = "b"; minFGroup.clear(); 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);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > bdiffs) { trashCode += "d"; 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];
+ }
+
+ //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
+ if(qual.getName() != ""){
+ qual.trimQScores(-1, rStart);
+ qual.trimQScores(fStart, -1);
+ }
+ success = minDiff;
+ //cout << "barcode = " << ipbarcodes[group].forward << '\t' << ipbarcodes[group].reverse << endl;
+ }else { if (trashCode == "") { trashCode = "bd"; } success = bdiffs + 100; }
+ }
+ //}
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ //catchall for case I didn't think of
+ if ((trashCode == "") && (success > bdiffs)) { trashCode = "bd"; }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripPairedBarcode");
+ exit(1);
+ }
+
+}
+//*******************************************************************/
+int TrimOligos::stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool keepForward){
+ try {
+ trashCode = "";
+ //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
+ trashCode = "p";
+ 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
+ trashCode += "q";
+ break;
+ }
+
+ if(compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) { //find forward
+ if (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()))) { //find reverse
+ group = it->first;
+ string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
+ seq.setUnaligned(trimmedSeq.substr(0,(trimmedSeq.length()-roligo.length()))); //trim reverse barcode
+ if(qual.getName() != ""){
+ qual.trimQScores(-1, rawSeq.length()-roligo.length());
+ qual.trimQScores(foligo.length(), -1);
+ }
+ success = 0;
+ trashCode = "";
+ return success;
+ }
+ }else {
+ trashCode = "b";
+ if (!compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()))) { trashCode += "d"; }
+ }
+
+ }
+ //cout << "success=" << success << endl;
+ //if you found the barcode or if you don't want to allow for diffs
+ if (pdiffs == 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()+bdiffs) << 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) { trashCode = "p"; minFGroup.clear(); 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);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > pdiffs) { trashCode += "q"; 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];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ if (!keepForward) {
+ string trimmedSeq = rawSeq.substr(0, rStart); //trim reverse barcode
+ seq.setUnaligned(trimmedSeq.substr(fStart)); //trim forward barcode
+ if(qual.getName() != ""){
+ qual.trimQScores(-1, rStart);
+ qual.trimQScores(fStart, -1);
+ }
+ }
+ success = minDiff;
+ //cout << "primer = " << ipprimers[group].forward << '\t' << ipprimers[group].reverse << endl;
+ }else { if (trashCode == "") { trashCode = "pq"; } success = pdiffs + 100; }
+ }
+ //}
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ //catchall for case I didn't think of
+ if ((trashCode == "") && (success > pdiffs)) { trashCode = "pq"; }
+
+ 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 {
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
+
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipprimers.begin();it!=ipprimers.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ if(rawFSequence.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(rawRSequence.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((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ forwardQual.trimQScores(foligo.length(), -1);
+ reverseQual.trimQScores(-1, rawRSequence.length()-roligo.length());
+ success = 0;
+ break;
+ }
+ }
+
+ //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(rawFSequence.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+pdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawFSequence.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 (irbarcodes.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;
+
+ for(map<string, vector<int> >::iterator it=irprimers.begin();it!=irprimers.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << 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 << "after = " << oligo << '\t' << 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);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ 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 = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ forwardQual.trimQScores(fStart, -1);
+ reverseQual.trimQScores(rStart, -1);
+ success = minDiff;
+ }else { success = pdiffs + 100; }
+ }
}
if (alignment != NULL) { delete alignment; }
-
}
return success;
}
catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripBarcode");
+ m->errorOut(e, "TrimOligos", "stripIForward");
exit(1);
}
}
-/*******************************************************************
-int TrimOligos::stripRBarcode(Sequence& seq, QualityScores& qual, int& group){
+//*******************************************************************/
+int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, int& group){
try {
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
- string rawSequence = seq.getUnaligned();
- int success = bdiffs + 1; //guilty until proven innocent
-
- //can you find the barcode
- for(map<string,int>::iterator it=rbarcodes.begin();it!=rbarcodes.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.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
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipprimers.begin();it!=ipprimers.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ if(rawFSequence.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(compareDNASeq(oligo, rawSequence.substr((rawSequence.length()-oligo.length()),oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(0,(rawSequence.length()-oligo.length())));
-
- if(qual.getName() != ""){
- qual.trimQScores(-1, rawSequence.length()-oligo.length());
- }
-
+ if(rawRSequence.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((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
success = 0;
break;
}
}
//if you found the barcode or if you don't want to allow for diffs
- if ((bdiffs == 0) || (success == 0)) { return success; }
-
+ if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (rbarcodes.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=rbarcodes.begin();it!=rbarcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
+ 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;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=rbarcodes.begin();it!=rbarcodes.end();it++){
+ 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;
- // int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
- success = bdiffs + 10;
+ if(rawFSequence.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
break;
}
-
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+pdiffs) << endl;
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr((rawSequence.length()-(oligo.length()+bdiffs)),oligo.length()+bdiffs));
+ alignment->alignPrimer(oligo, rawFSequence.substr(0,oligo.length()+pdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
-
+
int alnLength = oligo.length();
- for(int i=0;i<alnLength;i++){
- if(oligo[i] != '-'){ alnLength = i; break; }
- }
- oligo = oligo.substr(alnLength);
- temp = temp.substr(alnLength);
-
- int numDiff = countDiffs(oligo, temp);
+ 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;
- minGroup = it->second;
- minPos = 0;
- for(int i=alnLength-1;i>=0;i--){
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
- minPos++;
+ 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);
}
- else if(numDiff == minDiff){
- minCount++;
- }
-
}
-
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(0, (rawSequence.length()-minPos)));
+
+ //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(qual.getName() != ""){
- qual.trimQScores(-1, (rawSequence.length()-minPos));
- }
- success = minDiff;
+ if (irbarcodes.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;
+
+ for(map<string, vector<int> >::iterator it=irprimers.begin();it!=irprimers.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << 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 << "after = " << oligo << '\t' << 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);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ 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 = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ success = minDiff;
+ }else { success = pdiffs + 100; }
+ }
}
if (alignment != NULL) { delete alignment; }
-
}
return success;
}
catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripRBarcode");
+ m->errorOut(e, "TrimOligos", "stripIForward");
exit(1);
}
}
-/*******************************************************************
-int TrimOligos::stripRBarcode(Sequence& seq, int& group){
+//*******************************************************************/
+int TrimOligos::stripBarcode(Sequence& seq, int& group){
try {
string rawSequence = seq.getUnaligned();
int success = bdiffs + 1; //guilty until proven innocent
//can you find the barcode
- for(map<string,int>::iterator it=rbarcodes.begin();it!=rbarcodes.end();it++){
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
string oligo = it->first;
if(rawSequence.length() < oligo.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(compareDNASeq(oligo, rawSequence.substr((rawSequence.length()-oligo.length()),oligo.length()))){
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
group = it->second;
- seq.setUnaligned(rawSequence.substr(0,(rawSequence.length()-oligo.length())));
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
success = 0;
break;
if ((bdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
- Alignment* alignment;
- if (rbarcodes.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=rbarcodes.begin();it!=rbarcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
+ Alignment* alignment;
+ if (barcodes.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 minGroup = -1;
int minPos = 0;
- for(map<string,int>::iterator it=rbarcodes.begin();it!=rbarcodes.end();it++){
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxFBarcodeLength){ //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->align(oligo, rawSequence.substr((rawSequence.length()-(oligo.length()+bdiffs)),oligo.length()+bdiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
-
+
int alnLength = oligo.length();
- for(int i=0;i<alnLength;i++){
- if(oligo[i] != '-'){ alnLength = i; break; }
+ for(int i=oligo.length()-1;i>=0;i--){
+ if(oligo[i] != '-'){ alnLength = i+1; break; }
}
- oligo = oligo.substr(alnLength);
- temp = temp.substr(alnLength);
-
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
minCount = 1;
minGroup = it->second;
minPos = 0;
- for(int i=alnLength-1;i>=0;i--){
+ for(int i=0;i<alnLength;i++){
if(temp[i] != '-'){
minPos++;
}
else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
else{ //use the best match
group = minGroup;
- seq.setUnaligned(rawSequence.substr(0, (rawSequence.length()-minPos)));
-
+ seq.setUnaligned(rawSequence.substr(minPos));
success = minDiff;
}
}
catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripRBarcode");
+ m->errorOut(e, "TrimOligos", "stripBarcode");
exit(1);
}
}
-//********************************************************************/
+
+/********************************************************************/
int TrimOligos::stripForward(Sequence& seq, int& group){
try {
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (primers.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=primers.begin();it!=primers.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
-
- }else{ alignment = NULL; }
+ if (primers.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;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){
+ if(rawSequence.length() < maxFPrimerLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
//*******************************************************************/
int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group, bool keepForward){
try {
+
+ if (paired) { int success = stripPairedPrimers(seq, qual, group, keepForward); return success; }
+
string rawSequence = seq.getUnaligned();
int success = pdiffs + 1; //guilty until proven innocent
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (primers.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=primers.begin();it!=primers.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
-
- }else{ alignment = NULL; }
+ if (primers.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;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){
+ if(rawSequence.length() < maxFPrimerLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
if ((ldiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (linker.size() > 0) {
- for(int i = 0; i < linker.size(); i++){
- if(linker[i].length() > maxLength){
- maxLength = linker[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+ldiffs+1));
-
- }else{ alignment = NULL; }
+ if (linker.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLinkerLength+ldiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = linker[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
success = ldiffs + 10;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
if ((ldiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (linker.size() > 0) {
- for(int i = 0; i < linker.size(); i++){
- if(linker[i].length() > maxLength){
- maxLength = linker[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+ldiffs+1));
-
- }else{ alignment = NULL; }
+ if (linker.size() > 0) {alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLinkerLength+ldiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = linker[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
success = ldiffs + 10;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
if ((sdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (spacer.size() > 0) {
- for(int i = 0; i < spacer.size(); i++){
- if(spacer[i].length() > maxLength){
- maxLength = spacer[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+sdiffs+1));
-
- }else{ alignment = NULL; }
+ if (spacer.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxSpacerLength+sdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = spacer[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
success = sdiffs + 10;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
if ((sdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (spacer.size() > 0) {
- for(int i = 0; i < spacer.size(); i++){
- if(spacer[i].length() > maxLength){
- maxLength = spacer[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+sdiffs+1));
-
- }else{ alignment = NULL; }
+ if (spacer.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxSpacerLength+sdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = spacer[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
success = sdiffs + 10;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
exit(1);
}
}
+//********************************************************************/
+string TrimOligos::reverseOligo(string oligo){
+ try {
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else if(oligo[i] == '-'){ reverse += '-'; }
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "reverseOligo");
+ exit(1);
+ }
+}
+
/********************************************************************/
projects / mothur.git / blobdiff