void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, allFiles, createGroup;
- string outputDir, ffastqfile, rfastqfile, align, oligosfile;
+ bool abort, allFiles, trimOverlap, createFileGroup, createOligosGroup, makeCount;
+ string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file, format;
float match, misMatch, gapOpen, gapExtend;
- int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
+ int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq;
vector<string> outputNames;
map<int, oligosPair> barcodes;
vector<string> linker;
vector<string> spacer;
vector<string> primerNameVector;
- vector<string> barcodeNameVector;
+ vector<string> barcodeNameVector;
+ vector<char> convertTable;
map<string, int> groupCounts;
map<string, string> groupMap;
- //map<string, int> combos;
- //map<string, int> groupToIndex;
- //vector<string> groupVector;
+ map<int, string> file2Group;
+ vector<int> convertQual(string);
fastqRead readFastq(ifstream&, bool&);
- vector< vector<string> > readFastqFiles(int&);
- bool checkReads(fastqRead&, fastqRead&);
- 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> >&);
+ vector< vector< vector<string> > > preProcessData(unsigned long int&);
+ vector< vector<string> > readFileNames(string);
+ vector< vector<string> > readFastqFiles(unsigned long int&, string, string);
+ vector< vector<string> > readFastaFiles(unsigned long int&, string, string);
+ //bool checkReads(fastqRead&, fastqRead&, string, string);
+ int createProcesses(vector< vector<string> >, string, string, string, vector<vector<string> >, int);
+ int driver(vector<string>, string, string, string, vector<vector<string> >, int, string);
+ bool getOligos(vector<vector<string> >&, string);
string reverseOligo(string);
vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques);
};
// that can be passed using a single void pointer (LPVOID).
struct contigsData {
string outputFasta;
- string outputQual;
string outputScrapFasta;
- string outputScrapQual;
string outputMisMatches;
- string align;
+ string align, group;
vector<string> files;
vector<vector<string> > fastaFileNames;
- vector<vector<string> > qualFileNames;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
- int count, threshold, threadID, pdiffs, bdiffs, tdiffs;
- bool allFiles, createGroup;
+ int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq;
+ bool allFiles, createOligosGroup, createFileGroup, done, trimOverlap;
map<string, int> groupCounts;
map<string, string> groupMap;
vector<string> primerNameVector;
map<int, oligosPair> primers;
contigsData(){}
- 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) {
+ contigsData(string g, vector<string> f, string of, string osf, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, map<int, oligosPair> br, map<int, oligosPair> pr, vector<vector<string> > ffn, vector<string>bnv, vector<string> pnv, int pdf, int bdf, int tdf, bool cg, bool cfg, bool all, bool to, int tid) {
files = f;
outputFasta = of;
- outputQual = oq;
outputMisMatches = om;
m = mout;
match = ma;
misMatch = misMa;
gapOpen = gapO;
gapExtend = gapE;
- threshold = thr;
+ insert = thr;
align = al;
+ group = g;
count = 0;
outputScrapFasta = osf;
- outputScrapQual = osq;
fastaFileNames = ffn;
- qualFileNames = qfn;
barcodes = br;
primers = pr;
barcodeNameVector = bnv;
bdiffs = bdf;
tdiffs = tdf;
allFiles = all;
- createGroup = cg;
+ trimOverlap = to;
+ createOligosGroup = cg;
+ createFileGroup = cfg;
threadID = tid;
+ deltaq = delt;
+ done=false;
}
};
if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); }
else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase); }
- int num = 0;
+ pDataArray->count = 0;
string thisffastafile = pDataArray->files[0];
string thisfqualfile = pDataArray->files[1];
string thisrfastafile = pDataArray->files[2];
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;
+ ofstream outFasta, outMisMatch, outScrapFasta;
pDataArray->m->openInputFile(thisffastafile, inFFasta);
- pDataArray->m->openInputFile(thisfqualfile, inFQual);
pDataArray->m->openInputFile(thisrfastafile, inRFasta);
- pDataArray->m->openInputFile(thisrqualfile, inRQual);
-
- ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
+ if (thisfqualfile != "") {
+ pDataArray->m->openInputFile(thisfqualfile, inFQual);
+ pDataArray->m->openInputFile(thisrqualfile, inRQual);
+ }
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";
+
+ outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->primers, pDataArray->barcodes);
- while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+ while ((!inFFasta.eof()) && (!inRFasta.eof())) {
if (pDataArray->m->control_pressed) { break; }
//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);
+ QualityScores* fQual = NULL; QualityScores* rQual = NULL;
+ if (thisfqualfile != "") {
+ fQual = new QualityScores(inFQual); pDataArray->m->gobble(inFQual);
+ rQual = new QualityScores(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 (thisfqualfile != "") {
+ success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+ }else {
+ success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
+ }
if(success > pDataArray->bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(pDataArray->primers.size() != 0){
- success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex);
+ if (thisfqualfile != "") {
+ success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
+ }else {
+ success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
+ }
if(success > pDataArray->pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
//flip the reverse reads
rSeq.reverseComplement();
- rQual.flipQScores();
+ if (thisfqualfile != "") { rQual->flipQScores(); }
//pairwise align
alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
//traverse alignments merging into one contiguous seq
string contig = "";
- vector<int> contigScores;
int numMismatches = 0;
string seq1 = fSeq.getAligned();
string seq2 = rSeq.getAligned();
- vector<int> scores1 = fQual.getQualityScores();
- vector<int> scores2 = rQual.getQualityScores();
+ vector<int> scores1, scores2;
+ if (thisfqualfile != "") {
+ scores1 = fQual->getQualityScores();
+ scores2 = rQual->getQualityScores();
+ delete fQual; delete rQual;
+ }
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]]);
- }
+ for (int i = 0; i < overlapStart; i++) { contig += seq1[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]]);
- }
+ for (int i = 0; i < overlapStart; i++) { contig += seq2[i]; }
}
int seq1End = fSeq.getEndPos();
int overlapEnd = seq1End;
if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
+ int oStart = contig.length();
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[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) { } //
- 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) { } //
- else {
- contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[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 insert. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores2[BBaseMap[i]] < pDataArray->insert) { } //
+ else { contig += seq2[i]; }
+ }else { contig += seq2[i]; } //with no quality info, then we keep it?
+ }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 insert. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores1[ABaseMap[i]] < pDataArray->insert) { } //
+ else { contig += seq1[i]; }
+ }else { contig += seq1[i]; } //with no quality info, then we keep it?
}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[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
- contig += c;
- numMismatches++;
+ if (thisfqualfile != "") {
+ if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= pDataArray->deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
+ char c = seq1[i];
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
+ contig += c;
+ }else { //if no, base becomes n
+ contig += 'N';
+ }
+ numMismatches++;
+ }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
}else { //should never get here
pDataArray->m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
}
}
+ int oend = contig.length();
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]]);
- }
+ for (int i = overlapEnd; i < length; i++) { contig += seq2[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]]);
- }
-
+ for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
+ if (pDataArray->trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
+
if(trashCode.length() == 0){
- if (pDataArray->createGroup) {
+ bool ignore = false;
+ if (pDataArray->createOligosGroup) {
if(pDataArray->barcodes.size() != 0){
string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
if (pDataArray->primers.size() != 0) {
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] ++; }
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ 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] ++; }
+ }else { ignore = true; }
}
+ }else if (pDataArray->createFileGroup) {
+ int pos = pDataArray->group.find("ignore");
+ if (pos == string::npos) {
+ pDataArray->groupMap[fSeq.getName()] = pDataArray->group;
+
+ map<string, int>::iterator it = pDataArray->groupCounts.find(pDataArray->group);
+ if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[pDataArray->group] = 1; }
+ else { pDataArray->groupCounts[it->first]++; }
+ }else { ignore = true; }
}
+
- if(pDataArray->allFiles){
+ if(pDataArray->allFiles && !ignore){
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;
+ int numNs = 0;
+ for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; } }
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << 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++;
+ pDataArray->count++;
//report progress
- if((num) % 1000 == 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
}
//report progress
- if((num) % 1000 != 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
inFFasta.close();
- inFQual.close();
inRFasta.close();
- inRQual.close();
outFasta.close();
- outQual.close();
outMisMatch.close();
outScrapFasta.close();
- outScrapQual.close();
+ if (thisfqualfile != "") {
+ inFQual.close();
+ inRQual.close();
+ }
delete alignment;
- 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);}
+ pDataArray->done = true;
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta); }
return 0;
projects / mothur.git / blobdiff