--- /dev/null
+#ifndef CHIMERAPERSEUSCOMMAND_H
+#define CHIMERAPERSEUSCOMMAND_H
+
+
+/*
+ * chimeraperseuscommand.h
+ * Mothur
+ *
+ * Created by westcott on 10/26/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "mothur.h"
+#include "command.hpp"
+#include "sequenceparser.h"
+#include "myPerseus.h"
+
+/***********************************************************/
+class ChimeraPerseusCommand : public Command {
+public:
+ ChimeraPerseusCommand(string);
+ ChimeraPerseusCommand();
+ ~ChimeraPerseusCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "chimera.perseus"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Chimera.perseus\n"; }
+ string getDescription() { return "detect chimeric sequences"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ struct linePair {
+ int start;
+ int end;
+ linePair(int i, int j) : start(i), end(j) {}
+ };
+
+ bool abort;
+ string fastafile, groupfile, outputDir, namefile;
+ int processors, alignLength;
+ double cutoff, alpha, beta;
+
+ vector<string> outputNames;
+ vector<string> fastaFileNames;
+ vector<string> nameFileNames;
+ vector<string> groupFileNames;
+
+ string getNamesFile(string&);
+ int driver(string, vector<seqData>&, string, int&);
+ vector<seqData> readFiles(string, string);
+ vector<seqData> loadSequences(SequenceParser&, string);
+ int deconvoluteResults(SequenceParser&, string, string);
+ int driverGroups(SequenceParser&, string, string, int, int, vector<string>);
+ int createProcessesGroups(SequenceParser&, string, string, vector<string>, string, string, string);
+};
+
+/**************************************************************************************************/
+//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 perseusData {
+ string fastafile;
+ string namefile;
+ string groupfile;
+ string outputFName;
+ string accnos;
+ MothurOut* m;
+ int start;
+ int end;
+ int threadID, count, numChimeras;
+ double alpha, beta, cutoff;
+ vector<string> groups;
+
+ perseusData(){}
+ perseusData(double a, double b, double c, string o, string f, string n, string g, string ac, vector<string> gr, MothurOut* mout, int st, int en, int tid) {
+ alpha = a;
+ beta = b;
+ cutoff = c;
+ fastafile = f;
+ namefile = n;
+ groupfile = g;
+ outputFName = o;
+ accnos = ac;
+ m = mout;
+ start = st;
+ end = en;
+ threadID = tid;
+ groups = gr;
+ count = 0;
+ numChimeras = 0;
+ }
+};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
+ perseusData* pDataArray;
+ pDataArray = (perseusData*)lpParam;
+
+ try {
+
+ //clears files
+ ofstream out, out1, out2;
+ pDataArray->m->openOutputFile(pDataArray->outputFName, out); out.close();
+ pDataArray->m->openOutputFile(pDataArray->accnos, out1); out1.close();
+
+ //parse fasta and name file by group
+ SequenceParser* parser;
+ if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
+ else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile); }
+
+ int totalSeqs = 0;
+ int numChimeras = 0;
+
+ for (int i = pDataArray->start; i < pDataArray->end; i++) {
+
+ int start = time(NULL); if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
+
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Checking sequences from group " + pDataArray->groups[i] + "..."); pDataArray->m->mothurOutEndLine();
+
+ //vector<seqData> sequences = loadSequences(parser, groups[i]); - same function below
+ ////////////////////////////////////////////////////////////////////////////////////////
+ vector<Sequence> thisGroupsSeqs = parser->getSeqs(pDataArray->groups[i]);
+ map<string, string> nameMap = parser->getNameMap(pDataArray->groups[i]);
+ map<string, string>::iterator it;
+
+ vector<seqData> sequences;
+ bool error = false;
+
+ for (int j = 0; j < thisGroupsSeqs.size(); j++) {
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
+
+ it = nameMap.find(thisGroupsSeqs[j].getName());
+ if (it == nameMap.end()) { error = true; pDataArray->m->mothurOut("[ERROR]: " + thisGroupsSeqs[j].getName() + " is in your fasta file and not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
+ else {
+ int num = pDataArray->m->getNumNames(it->second);
+ sequences.push_back(seqData(thisGroupsSeqs[j].getName(), thisGroupsSeqs[j].getUnaligned(), num));
+ }
+ }
+
+ if (error) { pDataArray->m->control_pressed = true; }
+
+ //sort by frequency
+ sort(sequences.rbegin(), sequences.rend());
+ ////////////////////////////////////////////////////////////////////////////////////////
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
+
+ //int numSeqs = driver((outputFName + groups[i]), sequences, (accnos+groups[i]), numChimeras); - same function below
+ ////////////////////////////////////////////////////////////////////////////////////////
+ string chimeraFileName = pDataArray->outputFName+pDataArray->groups[i];
+ string accnosFileName = pDataArray->accnos+pDataArray->groups[i];
+
+ vector<vector<double> > correctModel(4); //could be an option in the future to input own model matrix
+ for(int j=0;j<4;j++){ correctModel[j].resize(4); }
+
+ correctModel[0][0] = 0.000000; //AA
+ correctModel[1][0] = 11.619259; //CA
+ correctModel[2][0] = 11.694004; //TA
+ correctModel[3][0] = 7.748623; //GA
+
+ correctModel[1][1] = 0.000000; //CC
+ correctModel[2][1] = 7.619657; //TC
+ correctModel[3][1] = 12.852562; //GC
+
+ correctModel[2][2] = 0.000000; //TT
+ correctModel[3][2] = 10.964048; //TG
+
+ correctModel[3][3] = 0.000000; //GG
+
+ for(int k=0;k<4;k++){
+ for(int j=0;j<k;j++){
+ correctModel[j][k] = correctModel[k][j];
+ }
+ }
+
+ int numSeqs = sequences.size();
+ int alignLength = sequences[0].sequence.size();
+
+ ofstream chimeraFile;
+ ofstream accnosFile;
+ pDataArray->m->openOutputFile(chimeraFileName, chimeraFile);
+ pDataArray->m->openOutputFile(accnosFileName, accnosFile);
+
+ Perseus myPerseus;
+ vector<vector<double> > binMatrix = myPerseus.binomial(alignLength);
+
+ chimeraFile << "SequenceIndex\tName\tDiffsToBestMatch\tBestMatchIndex\tBestMatchName\tDiffstToChimera\tIndexofLeftParent\tIndexOfRightParent\tNameOfLeftParent\tNameOfRightParent\tDistanceToBestMatch\tcIndex\t(cIndex - singleDist)\tloonIndex\tMismatchesToChimera\tMismatchToTrimera\tChimeraBreakPoint\tLogisticProbability\tTypeOfSequence\n";
+
+ vector<bool> chimeras(numSeqs, 0);
+
+ for(int j=0;j<numSeqs;j++){
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ vector<bool> restricted = chimeras;
+
+ vector<vector<int> > leftDiffs(numSeqs);
+ vector<vector<int> > leftMaps(numSeqs);
+ vector<vector<int> > rightDiffs(numSeqs);
+ vector<vector<int> > rightMaps(numSeqs);
+
+ vector<int> singleLeft, bestLeft;
+ vector<int> singleRight, bestRight;
+
+ int bestSingleIndex, bestSingleDiff;
+ vector<pwAlign> alignments(numSeqs);
+
+ int comparisons = myPerseus.getAlignments(j, sequences, alignments, leftDiffs, leftMaps, rightDiffs, rightMaps, bestSingleIndex, bestSingleDiff, restricted);
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ int minMismatchToChimera, leftParentBi, rightParentBi, breakPointBi;
+
+ string dummyA, dummyB;
+
+ if(comparisons >= 2){
+ minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ int minMismatchToTrimera = numeric_limits<int>::max();
+ int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
+
+ if(minMismatchToChimera >= 3 && comparisons >= 3){
+ minMismatchToTrimera = myPerseus.getTrimera(sequences, leftDiffs, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight, restricted);
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+ }
+
+ double singleDist = myPerseus.modeledPairwiseAlignSeqs(sequences[j].sequence, sequences[bestSingleIndex].sequence, dummyA, dummyB, correctModel);
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ string type;
+ string chimeraRefSeq;
+
+ if(minMismatchToChimera - minMismatchToTrimera >= 3){
+ type = "trimera";
+ chimeraRefSeq = myPerseus.stitchTrimera(alignments, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, leftMaps, rightMaps);
+ }
+ else{
+ type = "chimera";
+ chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, leftMaps, rightMaps);
+ }
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ double chimeraDist = myPerseus.modeledPairwiseAlignSeqs(sequences[j].sequence, chimeraRefSeq, dummyA, dummyB, correctModel);
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ double cIndex = chimeraDist;//modeledPairwiseAlignSeqs(sequences[j].sequence, chimeraRefSeq);
+ double loonIndex = myPerseus.calcLoonIndex(sequences[j].sequence, sequences[leftParentBi].sequence, sequences[rightParentBi].sequence, breakPointBi, binMatrix);
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); chimeraFile.close(); pDataArray->m->mothurRemove(chimeraFileName); accnosFile.close(); pDataArray->m->mothurRemove(accnosFileName); return 0; }
+
+ chimeraFile << j << '\t' << sequences[j].seqName << '\t' << bestSingleDiff << '\t' << bestSingleIndex << '\t' << sequences[bestSingleIndex].seqName << '\t';
+ chimeraFile << minMismatchToChimera << '\t' << leftParentBi << '\t' << rightParentBi << '\t' << sequences[leftParentBi].seqName << '\t' << sequences[rightParentBi].seqName << '\t';
+ chimeraFile << singleDist << '\t' << cIndex << '\t' << (cIndex - singleDist) << '\t' << loonIndex << '\t';
+ chimeraFile << minMismatchToChimera << '\t' << minMismatchToTrimera << '\t' << breakPointBi << '\t';
+
+ double probability = myPerseus.classifyChimera(singleDist, cIndex, loonIndex, pDataArray->alpha, pDataArray->beta);
+
+ chimeraFile << probability << '\t';
+
+ if(probability > pDataArray->cutoff){
+ chimeraFile << type << endl;
+ accnosFile << sequences[j].seqName << endl;
+ chimeras[j] = 1;
+ numChimeras++;
+ }
+ else{
+ chimeraFile << "good" << endl;
+ }
+
+ }
+ else{
+ chimeraFile << j << '\t' << sequences[j].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
+ }
+ //report progress
+ if((j+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(j+1) + "\n"); }
+ }
+
+ if((numSeqs) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n"); }
+
+ chimeraFile.close();
+ accnosFile.close();
+ ////////////////////////////////////////////////////////////////////////////////////////
+
+ totalSeqs += numSeqs;
+
+ //append files
+ pDataArray->m->appendFiles(chimeraFileName, pDataArray->outputFName); pDataArray->m->mothurRemove(chimeraFileName);
+ pDataArray->m->appendFiles(accnosFileName, pDataArray->accnos); pDataArray->m->mothurRemove(accnosFileName);
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + pDataArray->groups[i] + "."); pDataArray->m->mothurOutEndLine();
+
+ if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
+ }
+
+ pDataArray->count = totalSeqs;
+ delete parser;
+ return totalSeqs;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ChimeraUchimeCommand", "MyPerseusThreadFunction");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+#endif
+
+#endif
+
+
projects / mothur.git / blobdiff