#include "qualityscores.h"
#include "trimoligos.h"
#include "counttable.h"
+#include "oligos.h"
class TrimSeqsCommand : public Command {
linePair() {}
};
- bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
+ Oligos oligos;
+ bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&, map<string, string>&);
bool keepFirstTrim(Sequence&, QualityScores&);
bool removeLastTrim(Sequence&, QualityScores&);
bool cullLength(Sequence&);
bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
- string reverseOligo(string);
-
bool abort, createGroup;
string fastaFile, oligoFile, qFileName, groupfile, nameFile, countfile, outputDir;
- bool flip, allFiles, qtrim, keepforward, pairedOligos, reorient;
- int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
+ bool flip, allFiles, qtrim, keepforward, pairedOligos, reorient, logtransform;
+ int numBarcodes, numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
int qWindowSize, qWindowStep, keepFirst, removeLast;
double qRollAverage, qThreshold, qWindowAverage, qAverage;
- vector<string> revPrimer, outputNames;
set<string> filesToRemove;
- map<int, oligosPair> pairedBarcodes;
- map<int, oligosPair> pairedPrimers;
- map<string, int> barcodes;
- vector<string> groupVector;
- map<string, int> primers;
- vector<string> linker;
- vector<string> spacer;
- map<string, int> combos;
- map<string, int> groupToIndex;
- vector<string> primerNameVector; //needed here?
- vector<string> barcodeNameVector; //needed here?
+ vector<string> groupVector,outputNames;
map<string, int> groupCounts;
map<string, string> nameMap;
map<string, int> nameCount; //for countfile name -> repCount
struct trimData {
unsigned long long start, end;
MothurOut* m;
- string filename, qFileName, trimFileName, scrapFileName, trimQFileName, scrapQFileName, trimNFileName, scrapNFileName, trimCFileName, scrapCFileName, groupFileName, nameFile, countfile;
+ string filename, qFileName, oligosfile, trimFileName, scrapFileName, trimQFileName, scrapQFileName, trimNFileName, scrapNFileName, trimCFileName, scrapCFileName, groupFileName, nameFile, countfile;
vector<vector<string> > fastaFileNames;
vector<vector<string> > qualFileNames;
vector<vector<string> > nameFileNames;
unsigned long long lineStart, lineEnd, qlineStart, qlineEnd;
- bool flip, allFiles, qtrim, keepforward, createGroup, pairedOligos, reorient;
- int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
+ bool flip, allFiles, qtrim, keepforward, createGroup, reorient, logtransform;
+ int maxAmbig, maxHomoP, minLength, maxLength, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
int qWindowSize, qWindowStep, keepFirst, removeLast, count;
double qRollAverage, qThreshold, qWindowAverage, qAverage;
- vector<string> revPrimer;
- map<string, int> barcodes;
- map<string, int> primers;
map<string, int> nameCount;
- vector<string> linker;
- vector<string> spacer;
- map<string, int> combos;
- vector<string> primerNameVector;
- vector<string> barcodeNameVector;
map<string, int> groupCounts;
map<string, string> nameMap;
map<string, string> groupMap;
- map<int, oligosPair> pairedBarcodes;
- map<int, oligosPair> pairedPrimers;
trimData(){}
trimData(string fn, string qn, string nf, string cf, string tn, string sn, string tqn, string sqn, string tnn, string snn, string tcn, string scn,string gn, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<vector<string> > nfn, unsigned long long lstart, unsigned long long lend, unsigned long long qstart, unsigned long long qend, MothurOut* mout,
- int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, vector<string> revP, vector<string> li, vector<string> spa, map<int, oligosPair> pbr, map<int, oligosPair> ppr, bool po,
- vector<string> priNameVector, vector<string> barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
- int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage,
+ int pd, int bd, int ld, int sd, int td, string o, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
+ int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage, bool lt,
int minL, int maxA, int maxH, int maxL, bool fli, bool reo, map<string, string> nm, map<string, int> ncount) {
filename = fn;
qFileName = qn;
qlineEnd = qend;
m = mout;
nameCount = ncount;
+ oligosfile = o;
pdiffs = pd;
bdiffs = bd;
ldiffs = ld;
sdiffs = sd;
tdiffs = td;
- barcodes = bar;
- pairedPrimers = ppr;
- pairedBarcodes = pbr;
- pairedOligos = po;
- primers = pri; numFPrimers = primers.size();
- revPrimer = revP; numRPrimers = revPrimer.size();
- linker = li; numLinkers = linker.size();
- spacer = spa; numSpacers = spacer.size();
- primerNameVector = priNameVector;
- barcodeNameVector = barNameVector;
createGroup = cGroup;
allFiles = aFiles;
qThreshold = Threshold;
qAverage = Average;
qRollAverage = RollAverage;
+ logtransform = lt;
minLength = minL;
maxAmbig = maxA;
maxHomoP = maxH;
}
}
+ int numBarcodes, numLinkers, numSpacers, numRPrimers, numFPrimers;
+ bool pairedOligos;
+ Oligos oligos(pDataArray->oligosfile);
+ if (oligos.hasPairedBarcodes()) {
+ pairedOligos = true;
+ numFPrimers = oligos.getPairedPrimers().size();
+ numBarcodes = oligos.getPairedBarcodes().size();
+ }else {
+ pairedOligos = false;
+ numFPrimers = oligos.getPrimers().size();
+ numBarcodes = oligos.getBarcodes().size();
+ }
+
+ numLinkers = oligos.getLinkers().size();
+ numSpacers = oligos.getSpacers().size();
+ numRPrimers = oligos.getReversePrimers().size();
+
TrimOligos* trimOligos = NULL;
- int numBarcodes = pDataArray->barcodes.size();
- if (pDataArray->pairedOligos) { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes); numBarcodes = pDataArray->pairedBarcodes.size(); }
- else { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer); }
+ if (pairedOligos) { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes()); }
+ else { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, oligos.getPrimers(), oligos.getBarcodes(), oligos.getReversePrimers(), oligos.getLinkers(), oligos.getSpacers()); }
TrimOligos* rtrimOligos = NULL;
if (pDataArray->reorient) {
- //create reoriented primer and barcode pairs
- map<int, oligosPair> rpairedPrimers, rpairedBarcodes;
- for (map<int, oligosPair>::iterator it = pDataArray->pairedPrimers.begin(); it != pDataArray->pairedPrimers.end(); it++) {
- oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
- rpairedPrimers[it->first] = tempPair;
- }
- for (map<int, oligosPair>::iterator it = pDataArray->pairedBarcodes.begin(); it != pDataArray->pairedBarcodes.end(); it++) {
- oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
- rpairedBarcodes[it->first] = tempPair;
- }
- rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();
+ rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes()); numBarcodes = oligos.getReorientedPairedBarcodes().size();
}
pDataArray->count = 0;
for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
if (pDataArray->m->control_pressed) {
- delete trimOligos;
+ delete trimOligos; if (pDataArray->reorient) { delete rtrimOligos; }
inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
if ((pDataArray->createGroup) && (pDataArray->countfile == "")) { outGroupsFile.close(); }
if(pDataArray->qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);
+ Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
- QualityScores currQual;
+ QualityScores currQual; QualityScores savedQual;
if(pDataArray->qFileName != ""){
currQual = QualityScores(qFile); pDataArray->m->gobble(qFile);
+ savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
}
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
int barcodeIndex = 0;
int primerIndex = 0;
- if(pDataArray->numLinkers != 0){
+ if(numLinkers != 0){
success = trimOligos->stripLinker(currSeq, currQual);
if(success > pDataArray->ldiffs) { trashCode += 'k'; }
else{ currentSeqsDiffs += success; }
else{ currentSeqsDiffs += success; }
}
- if(pDataArray->numSpacers != 0){
+ if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq, currQual);
if(success > pDataArray->sdiffs) { trashCode += 's'; }
else{ currentSeqsDiffs += success; }
}
- if(pDataArray->numFPrimers != 0){
+ if(numFPrimers != 0){
success = trimOligos->stripForward(currSeq, currQual, primerIndex, pDataArray->keepforward);
if(success > pDataArray->pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
if (currentSeqsDiffs > pDataArray->tdiffs) { trashCode += 't'; }
- if(pDataArray->numRPrimers != 0){
+ if(numRPrimers != 0){
success = trimOligos->stripReverse(currSeq, currQual);
if(!success) { trashCode += 'r'; }
}
int thisPrimerIndex = 0;
if(numBarcodes != 0){
- thisSuccess = rtrimOligos->stripBarcode(currSeq, currQual, thisBarcodeIndex);
+ thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
if(thisSuccess > pDataArray->bdiffs) { thisTrashCode += 'b'; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
- if(pDataArray->numFPrimers != 0){
- thisSuccess = rtrimOligos->stripForward(currSeq, currQual, thisPrimerIndex, pDataArray->keepforward);
+ if(numFPrimers != 0){
+ thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, pDataArray->keepforward);
if(thisSuccess > pDataArray->pdiffs) { thisTrashCode += 'f'; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
currentSeqsDiffs = thisCurrentSeqsDiffs;
barcodeIndex = thisBarcodeIndex;
primerIndex = thisPrimerIndex;
- }
+ savedSeq.reverseComplement();
+ currSeq.setAligned(savedSeq.getAligned());
+ if(pDataArray->qFileName != ""){
+ savedQual.flipQScores();
+ currQual.setScores(savedQual.getScores());
+ }
+ }else { trashCode += "(" + thisTrashCode + ")"; }
}
int origLength = currSeq.getNumBases();
if(pDataArray->qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, pDataArray->qThreshold); }
- else if(pDataArray->qAverage != 0) { success = currQual.cullQualAverage(currSeq, pDataArray->qAverage); }
- else if(pDataArray->qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, pDataArray->qRollAverage); }
- else if(pDataArray->qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, pDataArray->qWindowStep, pDataArray->qWindowSize, pDataArray->qWindowAverage); }
+ else if(pDataArray->qAverage != 0) { success = currQual.cullQualAverage(currSeq, pDataArray->qAverage, pDataArray->logtransform); }
+ else if(pDataArray->qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, pDataArray->qRollAverage, pDataArray->logtransform); }
+ else if(pDataArray->qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, pDataArray->qWindowStep, pDataArray->qWindowSize, pDataArray->qWindowAverage, pDataArray->logtransform); }
else { success = 1; }
//you don't want to trim, if it fails above then scrap it
if(trashCode.length() == 0){
string thisGroup = "";
- if (pDataArray->createGroup) {
- if(numBarcodes != 0){
- thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
- if (pDataArray->numFPrimers != 0) {
- if (pDataArray->primerNameVector[primerIndex] != "") {
- if(thisGroup != "") {
- thisGroup += "." + pDataArray->primerNameVector[primerIndex];
- }else {
- thisGroup = pDataArray->primerNameVector[primerIndex];
- }
- }
- }
- }
- }
+ if (pDataArray->createGroup) { thisGroup = oligos.getGroupName(barcodeIndex, primerIndex); }
int pos = thisGroup.find("ignore");
if (pos == string::npos) {
}
//report progress
- if((i) % 1000 == 0){ pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
}
//report progress
if((pDataArray->count) % 1000 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+ if (pDataArray->reorient) { delete rtrimOligos; }
delete trimOligos;
inFASTA.close();
trimFASTAFile.close();
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