~fastqRead() {};
};
+struct pairFastqRead {
+ fastqRead forward;
+ fastqRead reverse;
+
+ pairFastqRead() {};
+ pairFastqRead(fastqRead f, fastqRead r) : forward(f), reverse(r){};
+ ~pairFastqRead() {};
+};
/**************************************************************************************************/
class MakeContigsCommand : public Command {
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, allFiles;
+ bool abort, allFiles, createGroup;
string outputDir, ffastqfile, rfastqfile, align, oligosfile;
float match, misMatch, gapOpen, gapExtend;
int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
vector<string> primerNameVector;
vector<string> barcodeNameVector;
- map<string, int> groupCounts;
+ map<string, int> groupCounts;
+ map<string, string> groupMap;
//map<string, int> combos;
//map<string, int> groupToIndex;
//vector<string> groupVector;
- fastqRead readFastq(ifstream&);
+ fastqRead readFastq(ifstream&, bool&);
vector< vector<string> > readFastqFiles(int&);
bool checkReads(fastqRead&, fastqRead&);
- int createProcesses(vector< vector<string> >, string, string, string);
- int driver(vector<string>, string, string, string);
+ int createProcesses(vector< vector<string> >, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
+ int driver(vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
bool getOligos(vector<vector<string> >&, vector<vector<string> >&);
string reverseOligo(string);
+ vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques);
};
/**************************************************************************************************/
struct contigsData {
string outputFasta;
string outputQual;
+ string outputScrapFasta;
+ string outputScrapQual;
string outputMisMatches;
string align;
vector<string> files;
+ vector<vector<string> > fastaFileNames;
+ vector<vector<string> > qualFileNames;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
- int count, threshold, threadID;
+ int count, threshold, threadID, pdiffs, bdiffs, tdiffs;
+ bool allFiles, createGroup;
+ map<string, int> groupCounts;
+ map<string, string> groupMap;
+ vector<string> primerNameVector;
+ vector<string> barcodeNameVector;
+ map<int, oligosPair> barcodes;
+ map<int, oligosPair> primers;
contigsData(){}
- contigsData(vector<string> f, string of, string oq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int tid) {
+ contigsData(vector<string> f, string of, string oq, string osf, string osq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, map<int, oligosPair> br, map<int, oligosPair> pr, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<string>bnv, vector<string> pnv, int pdf, int bdf, int tdf, bool cg, bool all, int tid) {
files = f;
outputFasta = of;
outputQual = oq;
threshold = thr;
align = al;
count = 0;
+ outputScrapFasta = osf;
+ outputScrapQual = osq;
+ fastaFileNames = ffn;
+ qualFileNames = qfn;
+ barcodes = br;
+ primers = pr;
+ barcodeNameVector = bnv;
+ primerNameVector = pnv;
+ pdiffs = pdf;
+ bdiffs = bdf;
+ tdiffs = tdf;
+ allFiles = all;
+ createGroup = cg;
threadID = tid;
}
};
if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+ if(pDataArray->allFiles){
+ for (int i = 0; i < pDataArray->fastaFileNames.size(); i++) { //clears old file
+ for (int j = 0; j < pDataArray->fastaFileNames[i].size(); j++) { //clears old file
+ if (pDataArray->fastaFileNames[i][j] != "") {
+ ofstream temp;
+ pDataArray->m->openOutputFile(pDataArray->fastaFileNames[i][j], temp); temp.close();
+ pDataArray->m->openOutputFile(pDataArray->qualFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
+ }
+
ifstream inFFasta, inRFasta, inFQual, inRQual;
pDataArray->m->openInputFile(thisffastafile, inFFasta);
pDataArray->m->openInputFile(thisfqualfile, inFQual);
pDataArray->m->openInputFile(thisrfastafile, inRFasta);
pDataArray->m->openInputFile(thisrqualfile, inRQual);
- ofstream outFasta, outQual, outMisMatch;
+ ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
pDataArray->m->openOutputFile(pDataArray->outputQual, outQual);
pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
+ pDataArray->m->openOutputFile(pDataArray->outputScrapFasta, outScrapFasta);
+ pDataArray->m->openOutputFile(pDataArray->outputScrapQual, outScrapQual);
outMisMatch << "Name\tLength\tMisMatches\n";
+ TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->primers, pDataArray->barcodes);
+
while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
if (pDataArray->m->control_pressed) { break; }
+ int success = 1;
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
+
//read seqs and quality info
Sequence fSeq(inFFasta); pDataArray->m->gobble(inFFasta);
Sequence rSeq(inRFasta); pDataArray->m->gobble(inRFasta);
QualityScores fQual(inFQual); pDataArray->m->gobble(inFQual);
QualityScores rQual(inRQual); pDataArray->m->gobble(inRQual);
+ int barcodeIndex = 0;
+ int primerIndex = 0;
+
+ if(pDataArray->barcodes.size() != 0){
+ success = trimOligos.stripBarcode(fSeq, rSeq, fQual, rQual, barcodeIndex);
+ if(success > pDataArray->bdiffs) { trashCode += 'b'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if(pDataArray->primers.size() != 0){
+ success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex);
+ if(success > pDataArray->pdiffs) { trashCode += 'f'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if (currentSeqsDiffs > pDataArray->tdiffs) { trashCode += 't'; }
+
//flip the reverse reads
rSeq.reverseComplement();
rQual.flipQScores();
-
+
//pairwise align
alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
int numMismatches = 0;
string seq1 = fSeq.getAligned();
string seq2 = rSeq.getAligned();
-
vector<int> scores1 = fQual.getQualityScores();
vector<int> scores2 = rQual.getQualityScores();
- for (int i = 0; i < length; i++) {
+ int overlapStart = fSeq.getStartPos();
+ int seq2Start = rSeq.getStartPos();
+ //bigger of the 2 starting positions is the location of the overlapping start
+ if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
+ overlapStart = seq2Start;
+ for (int i = 0; i < overlapStart; i++) {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+ }else { //seq1 starts later so take from 0 to overlapStart from seq2
+ for (int i = 0; i < overlapStart; i++) {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }
+
+ int seq1End = fSeq.getEndPos();
+ int seq2End = rSeq.getEndPos();
+ int overlapEnd = seq1End;
+ if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
+
+ for (int i = overlapStart; i < overlapEnd; i++) {
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; }
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
}else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
- if (scores2[BBaseMap[i]] >= pDataArray->threshold) {
+ if (scores2[BBaseMap[i]] < pDataArray->threshold) { } //
+ else {
contig += seq2[i];
contigScores.push_back(scores2[BBaseMap[i]]);
}
}else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
- if (scores1[ABaseMap[i]] >= pDataArray->threshold) {
+ if (scores1[ABaseMap[i]] < pDataArray->threshold) { } //
+ else {
contig += seq1[i];
contigScores.push_back(scores1[ABaseMap[i]]);
}
}else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
char c = seq1[i];
contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; c = seq2[i]; }
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
contig += c;
numMismatches++;
}else { //should never get here
}
}
- //output
- outFasta << ">" << fSeq.getName() << endl << contig << endl;
- outQual << ">" << fSeq.getName() << endl;
- for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
- outQual << endl;
- outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
-
+ if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
+ for (int i = overlapEnd; i < length; i++) {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }else { //seq2 ends before seq1 so take from overlap to length from seq1
+ for (int i = overlapEnd; i < length; i++) {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+
+ }
+
+ if(trashCode.length() == 0){
+ if (pDataArray->createGroup) {
+ if(pDataArray->barcodes.size() != 0){
+ string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
+ if (pDataArray->primers.size() != 0) {
+ if (pDataArray->primerNameVector[primerIndex] != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + pDataArray->primerNameVector[primerIndex];
+ }else {
+ thisGroup = pDataArray->primerNameVector[primerIndex];
+ }
+ }
+ }
+
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut(", group= " + thisGroup + "\n"); }
+
+ pDataArray->groupMap[fSeq.getName()] = thisGroup;
+
+ map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
+ if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1; }
+ else { pDataArray->groupCounts[it->first] ++; }
+
+ }
+ }
+
+ if(pDataArray->allFiles){
+ ofstream output;
+ pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
+ output << ">" << fSeq.getName() << endl << contig << endl;
+ output.close();
+
+ pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
+ output << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
+ output << endl;
+ output.close();
+ }
+
+ //output
+ outFasta << ">" << fSeq.getName() << endl << contig << endl;
+ outQual << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
+ outQual << endl;
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+ }else {
+ //output
+ outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
+ outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
+ outScrapQual << endl;
+ }
num++;
//report progress
outFasta.close();
outQual.close();
outMisMatch.close();
+ outScrapFasta.close();
+ outScrapQual.close();
delete alignment;
- if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches);}
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapQual); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta);}
return 0;
projects / mothur.git / blobdiff