#include "sequence.hpp"
#include "flowdata.h"
#include "groupmap.h"
+#include "trimoligos.h"
class TrimFlowsCommand : public Command {
public:
TrimFlowsCommand(string);
TrimFlowsCommand();
- ~TrimFlowsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~TrimFlowsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "trim.flows"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
+ string getDescription() { return "trim.flows"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
-// GroupMap* groupMap;
-
struct linePair {
- unsigned long int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
int comboStarts;
vector<int> processIDS; //processid
vector<linePair*> lines;
- vector<linePair*> qLines;
- map<string, vector<string> > outputTypes;
+
+ vector<unsigned long long> getFlowFileBreaks();
+ int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
+ int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
+ string reverseOligo(string);
+
vector<string> outputNames;
set<string> filesToRemove;
-
-
void getOligos(vector<vector<string> >&); //a rewrite of what is in trimseqscommand.h
- int stripBarcode(Sequence&, int&); //largely redundant with trimseqscommand.h
- int stripForward(Sequence&, int&); //largely redundant with trimseqscommand.h
- bool stripReverse(Sequence&); //largely redundant with trimseqscommand.h
- bool compareDNASeq(string, string); //largely redundant with trimseqscommand.h
- int countDiffs(string, string); //largely redundant with trimseqscommand.h
-
bool allFiles;
-// int processors;
+ int processors;
int numFPrimers, numRPrimers;
- int totalFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+ int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
+ int numFlows;
float signal, noise;
bool fasta;
-
+ string flowOrder;
string flowFileName, oligoFileName, outputDir;
-
map<string, int> barcodes;
map<string, int> primers;
vector<string> revPrimer;
+ vector<string> linker;
+ vector<string> spacer;
vector<string> primerNameVector; //needed here?
vector<string> barcodeNameVector; //needed here?
map<string, int> combos; //needed here?
map<string, int> groupToIndex; //needed here?
+};
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct trimFlowData {
+ string flowFileName;
+ string trimFlowFileName;
+ string scrapFlowFileName;
+ string fastaFileName;
+ string flowOrder;
+ vector<vector<string> > barcodePrimerComboFileNames;
+ map<string, int> barcodes;
+ map<string, int> primers;
+ vector<string> revPrimer;
+ bool fasta, allFiles;
+ unsigned long long start;
+ unsigned long long end;
+ MothurOut* m;
+ float signal, noise;
+ int numFlows, maxFlows, minFlows, maxHomoP, tdiffs, bdiffs, pdiffs, threadID, count;
- int driverCreateTrim(string, string, string, string);
-
-// int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>){};
- int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&){};
-
+ trimFlowData(){}
+ trimFlowData(string ff, string tf, string sf, string f, string fo, vector<vector<string> > bfn, map<string, int> bar, map<string, int> pri, vector<string> rev, bool fa, bool al, unsigned long long st, unsigned long long en, MothurOut* mout, float sig, float n, int numF, int maxF, int minF, int maxH, int td, int bd, int pd, int tid) {
+ flowFileName = ff;
+ trimFlowFileName = tf;
+ scrapFlowFileName = sf;
+ fastaFileName = f;
+ flowOrder = fo;
+ barcodePrimerComboFileNames = bfn;
+ barcodes = bar;
+ primers = pri;
+ revPrimer = rev;
+ fasta = fa;
+ allFiles = al;
+ start = st;
+ end = en;
+ m = mout;
+ signal = sig;
+ noise = n;
+ numFlows = numF;
+ maxFlows = maxF;
+ minFlows = minF;
+ maxHomoP = maxH;
+ tdiffs = td;
+ bdiffs = bd;
+ pdiffs = pd;
+ threadID = tid;
+ }
};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
+ trimFlowData* pDataArray;
+ pDataArray = (trimFlowData*)lpParam;
+
+ try {
+ ofstream trimFlowFile;
+ pDataArray->m->openOutputFile(pDataArray->trimFlowFileName, trimFlowFile);
+ trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
+
+ ofstream scrapFlowFile;
+ pDataArray->m->openOutputFile(pDataArray->scrapFlowFileName, scrapFlowFile);
+ scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
+
+ ofstream fastaFile;
+ if(pDataArray->fasta){ pDataArray->m->openOutputFile(pDataArray->fastaFileName, fastaFile); }
+
+ ifstream flowFile;
+ pDataArray->m->openInputFile(pDataArray->flowFileName, flowFile);
+
+ flowFile.seekg(pDataArray->start);
+
+ if(pDataArray->start == 0){
+ flowFile >> pDataArray->numFlows; pDataArray->m->gobble(flowFile);
+ scrapFlowFile << pDataArray->maxFlows << endl;
+ trimFlowFile << pDataArray->maxFlows << endl;
+ if(pDataArray->allFiles){
+ for(int i=0;i<pDataArray->barcodePrimerComboFileNames.size();i++){
+ for(int j=0;j<pDataArray->barcodePrimerComboFileNames[0].size();j++){
+ ofstream temp;
+ pDataArray->m->openOutputFile(pDataArray->barcodePrimerComboFileNames[i][j], temp);
+ temp << pDataArray->maxFlows << endl;
+ temp.close();
+ }
+ }
+ }
+ }
+
+ FlowData flowData(pDataArray->numFlows, pDataArray->signal, pDataArray->noise, pDataArray->maxHomoP, pDataArray->flowOrder);
+ cout << " thread flowdata address " << &flowData << '\t' << &flowFile << endl;
+ TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer);
+
+ pDataArray->count = pDataArray->end;
+ cout << pDataArray->threadID << '\t' << pDataArray->count << endl;
+ int count = 0;
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ if (pDataArray->m->control_pressed) { break; }
+ cout << pDataArray->threadID << '\t' << count << endl;
+ int success = 1;
+ int currentSeqDiffs = 0;
+ string trashCode = "";
+
+ flowData.getNext(flowFile);
+ cout << "thread good bit " << flowFile.good() << endl;
+ flowData.capFlows(pDataArray->maxFlows);
+
+ Sequence currSeq = flowData.getSequence();
+ if(!flowData.hasMinFlows(pDataArray->minFlows)){ //screen to see if sequence is of a minimum number of flows
+ success = 0;
+ trashCode += 'l';
+ }
+
+ int primerIndex = 0;
+ int barcodeIndex = 0;
+
+ if(pDataArray->barcodes.size() != 0){
+ success = trimOligos.stripBarcode(currSeq, barcodeIndex);
+ if(success > pDataArray->bdiffs) { trashCode += 'b'; }
+ else{ currentSeqDiffs += success; }
+ }
+
+ if(pDataArray->primers.size() != 0){
+ success = trimOligos.stripForward(currSeq, primerIndex);
+ if(success > pDataArray->pdiffs) { trashCode += 'f'; }
+ else{ currentSeqDiffs += success; }
+ }
+
+ if (currentSeqDiffs > pDataArray->tdiffs) { trashCode += 't'; }
+
+ if(pDataArray->revPrimer.size() != 0){
+ success = trimOligos.stripReverse(currSeq);
+ if(!success) { trashCode += 'r'; }
+ }
+
+ if(trashCode.length() == 0){
+
+ flowData.printFlows(trimFlowFile);
+
+ if(pDataArray->fasta) { currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile); }
+
+ if(pDataArray->allFiles){
+ ofstream output;
+ pDataArray->m->openOutputFileAppend(pDataArray->barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
+ output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
+
+ flowData.printFlows(output);
+ output.close();
+ }
+ }
+ else{
+ flowData.printFlows(scrapFlowFile, trashCode);
+ }
+
+ count++;
+ cout << pDataArray->threadID << '\t' << currSeq.getName() << endl;
+ //report progress
+ if((count) % 10000 == 0){ pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine(); }
+
+ }
+ //report progress
+ if((count) % 10000 != 0){ pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine(); }
+
+ trimFlowFile.close();
+ scrapFlowFile.close();
+ flowFile.close();
+ if(pDataArray->fasta){ fastaFile.close(); }
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "TrimFlowsCommand", "MyTrimFlowsThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
#endif
projects / mothur.git / blobdiff