vector<string> setParameters();
string getCommandName() { return "trim.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
string getDescription() { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
vector<string> revPrimer, outputNames;
set<string> filesToRemove;
map<string, int> barcodes;
- map<string, int> rbarcodes;
vector<string> groupVector;
map<string, int> primers;
vector<string> linker;
double qRollAverage, qThreshold, qWindowAverage, qAverage;
vector<string> revPrimer;
map<string, int> barcodes;
- map<string, int> rbarcodes;
map<string, int> primers;
map<string, int> nameCount;
vector<string> linker;
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, map<string, int> rbar, vector<string> revP, vector<string> li, vector<string> spa,
+ 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,
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 minL, int maxA, int maxH, int maxL, bool fli, map<string, string> nm, map<string, int> ncount) {
sdiffs = sd;
tdiffs = td;
barcodes = bar;
- rbarcodes = rbar;
primers = pri; numFPrimers = primers.size();
revPrimer = revP; numRPrimers = revPrimer.size();
linker = li; numLinkers = linker.size();
}
- TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->rbarcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
+ TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
pDataArray->count = pDataArray->lineEnd;
for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
else{ currentSeqsDiffs += success; }
}
- if(pDataArray->rbarcodes.size() != 0){
- success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
- if(success > pDataArray->bdiffs) { trashCode += 'b'; }
- else{ currentSeqsDiffs += success; }
- }
-
if(pDataArray->numSpacers != 0){
success = trimOligos.stripSpacer(currSeq, currQual);
if(success > pDataArray->sdiffs) { trashCode += 's'; }
}
if(trashCode.length() == 0){
- currSeq.setAligned(currSeq.getUnaligned());
- currSeq.printSequence(trimFASTAFile);
-
- if(pDataArray->qFileName != ""){
- currQual.printQScores(trimQualFile);
- }
-
- if(pDataArray->nameFile != ""){
- map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
- if (itName != pDataArray->nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
- else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
- }
-
- int numRedundants = 0;
- if (pDataArray->countfile != "") {
- map<string, int>::iterator itCount = pDataArray->nameCount.find(currSeq.getName());
- if (itCount != pDataArray->nameCount.end()) {
- trimCountFile << itCount->first << '\t' << itCount->second << endl;
- numRedundants = itCount->second-1;
- }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
- }
-
- if (pDataArray->createGroup) {
+ string thisGroup = "";
+ if (pDataArray->createGroup) {
if(pDataArray->barcodes.size() != 0){
string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
if (pDataArray->primers.size() != 0) {
}
}
}
-
- if (pDataArray->countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
- else { pDataArray->groupMap[currSeq.getName()] = thisGroup; }
-
- if (pDataArray->nameFile != "") {
- map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
- if (itName != pDataArray->nameMap.end()) {
- vector<string> thisSeqsNames;
- pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
- numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
- for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
- outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
- }
- }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
- }
-
- map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
- if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
- else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
+ }
+ }
+
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+
+ currSeq.setAligned(currSeq.getUnaligned());
+ currSeq.printSequence(trimFASTAFile);
+
+ if(pDataArray->qFileName != ""){
+ currQual.printQScores(trimQualFile);
+ }
+
+ if(pDataArray->nameFile != ""){
+ map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
+ if (itName != pDataArray->nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
+ else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
+ }
+
+ int numRedundants = 0;
+ if (pDataArray->countfile != "") {
+ map<string, int>::iterator itCount = pDataArray->nameCount.find(currSeq.getName());
+ if (itCount != pDataArray->nameCount.end()) {
+ trimCountFile << itCount->first << '\t' << itCount->second << endl;
+ numRedundants = itCount->second-1;
+ }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
+ }
+
+ if (pDataArray->createGroup) {
+ if(pDataArray->barcodes.size() != 0){
+
+ if (pDataArray->countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+ else { pDataArray->groupMap[currSeq.getName()] = thisGroup; }
+
+ if (pDataArray->nameFile != "") {
+ map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
+ if (itName != pDataArray->nameMap.end()) {
+ vector<string> thisSeqsNames;
+ pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
+ numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
+ for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+ outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+ }
+ }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
+ }
+
+ map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
+ if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
+ else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
+
+ }
+ }
+
+ if(pDataArray->allFiles){
+ ofstream output;
+ pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
+ currSeq.printSequence(output);
+ output.close();
- }
- }
-
- if(pDataArray->allFiles){
- ofstream output;
- pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
- currSeq.printSequence(output);
- output.close();
-
- if(pDataArray->qFileName != ""){
- pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
- currQual.printQScores(output);
- output.close();
- }
-
- if(pDataArray->nameFile != ""){
- map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
- if (itName != pDataArray->nameMap.end()) {
- pDataArray->m->openOutputFileAppend(pDataArray->nameFileNames[barcodeIndex][primerIndex], output);
- output << itName->first << '\t' << itName->second << endl;
- output.close();
- }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
- }
- }
+ if(pDataArray->qFileName != ""){
+ pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
+ currQual.printQScores(output);
+ output.close();
+ }
+
+ if(pDataArray->nameFile != ""){
+ map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
+ if (itName != pDataArray->nameMap.end()) {
+ pDataArray->m->openOutputFileAppend(pDataArray->nameFileNames[barcodeIndex][primerIndex], output);
+ output << itName->first << '\t' << itName->second << endl;
+ output.close();
+ }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
+ }
+ }
+ }
}
else{
if(pDataArray->nameFile != ""){ //needs to be before the currSeq name is changed
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