1 #ifndef CHIMERAPERSEUSCOMMAND_H
2 #define CHIMERAPERSEUSCOMMAND_H
6 * chimeraperseuscommand.h
9 * Created by westcott on 10/26/11.
10 * Copyright 2011 Schloss Lab. All rights reserved.
17 #include "command.hpp"
18 #include "sequenceparser.h"
19 #include "myPerseus.h"
21 /***********************************************************/
22 class ChimeraPerseusCommand : public Command {
24 ChimeraPerseusCommand(string);
25 ChimeraPerseusCommand();
26 ~ChimeraPerseusCommand() {}
28 vector<string> setParameters();
29 string getCommandName() { return "chimera.perseus"; }
30 string getCommandCategory() { return "Sequence Processing"; }
31 string getOutputFileNameTag(string, string);
32 string getHelpString();
33 string getCitation() { return "http://www.mothur.org/wiki/Chimera.perseus\n"; }
34 string getDescription() { return "detect chimeric sequences"; }
37 void help() { m->mothurOut(getHelpString()); }
43 linePair(int i, int j) : start(i), end(j) {}
47 string fastafile, groupfile, outputDir, namefile;
48 int processors, alignLength;
49 double cutoff, alpha, beta;
51 vector<string> outputNames;
52 vector<string> fastaFileNames;
53 vector<string> nameFileNames;
54 vector<string> groupFileNames;
56 string getNamesFile(string&);
57 int driver(string, vector<seqData>&, string, int&);
58 vector<seqData> readFiles(string, string);
59 vector<seqData> loadSequences(SequenceParser&, string);
60 int deconvoluteResults(SequenceParser&, string, string);
61 int driverGroups(SequenceParser&, string, string, int, int, vector<string>);
62 int createProcessesGroups(SequenceParser&, string, string, vector<string>, string, string, string);
65 /**************************************************************************************************/
66 //custom data structure for threads to use.
67 // This is passed by void pointer so it can be any data type
68 // that can be passed using a single void pointer (LPVOID).
78 int threadID, count, numChimeras;
79 double alpha, beta, cutoff;
80 vector<string> groups;
83 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) {
101 /**************************************************************************************************/
102 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
104 static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
105 perseusData* pDataArray;
106 pDataArray = (perseusData*)lpParam;
111 ofstream out, out1, out2;
112 pDataArray->m->openOutputFile(pDataArray->outputFName, out); out.close();
113 pDataArray->m->openOutputFile(pDataArray->accnos, out1); out1.close();
115 //parse fasta and name file by group
116 SequenceParser* parser;
117 if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
118 else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile); }
123 for (int i = pDataArray->start; i < pDataArray->end; i++) {
125 int start = time(NULL); if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
127 pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Checking sequences from group " + pDataArray->groups[i] + "..."); pDataArray->m->mothurOutEndLine();
129 //vector<seqData> sequences = loadSequences(parser, groups[i]); - same function below
130 ////////////////////////////////////////////////////////////////////////////////////////
131 vector<Sequence> thisGroupsSeqs = parser->getSeqs(pDataArray->groups[i]);
132 map<string, string> nameMap = parser->getNameMap(pDataArray->groups[i]);
133 map<string, string>::iterator it;
135 vector<seqData> sequences;
138 for (int j = 0; j < thisGroupsSeqs.size(); j++) {
140 if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
142 it = nameMap.find(thisGroupsSeqs[j].getName());
143 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(); }
145 int num = pDataArray->m->getNumNames(it->second);
146 sequences.push_back(seqData(thisGroupsSeqs[j].getName(), thisGroupsSeqs[j].getUnaligned(), num));
150 if (error) { pDataArray->m->control_pressed = true; }
153 sort(sequences.rbegin(), sequences.rend());
154 ////////////////////////////////////////////////////////////////////////////////////////
156 if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
158 //int numSeqs = driver((outputFName + groups[i]), sequences, (accnos+groups[i]), numChimeras); - same function below
159 ////////////////////////////////////////////////////////////////////////////////////////
160 string chimeraFileName = pDataArray->outputFName+pDataArray->groups[i];
161 string accnosFileName = pDataArray->accnos+pDataArray->groups[i];
163 vector<vector<double> > correctModel(4); //could be an option in the future to input own model matrix
164 for(int j=0;j<4;j++){ correctModel[j].resize(4); }
166 correctModel[0][0] = 0.000000; //AA
167 correctModel[1][0] = 11.619259; //CA
168 correctModel[2][0] = 11.694004; //TA
169 correctModel[3][0] = 7.748623; //GA
171 correctModel[1][1] = 0.000000; //CC
172 correctModel[2][1] = 7.619657; //TC
173 correctModel[3][1] = 12.852562; //GC
175 correctModel[2][2] = 0.000000; //TT
176 correctModel[3][2] = 10.964048; //TG
178 correctModel[3][3] = 0.000000; //GG
180 for(int k=0;k<4;k++){
181 for(int j=0;j<k;j++){
182 correctModel[j][k] = correctModel[k][j];
186 int numSeqs = sequences.size();
187 int alignLength = sequences[0].sequence.size();
189 ofstream chimeraFile;
191 pDataArray->m->openOutputFile(chimeraFileName, chimeraFile);
192 pDataArray->m->openOutputFile(accnosFileName, accnosFile);
195 vector<vector<double> > binMatrix = myPerseus.binomial(alignLength);
197 chimeraFile << "SequenceIndex\tName\tDiffsToBestMatch\tBestMatchIndex\tBestMatchName\tDiffstToChimera\tIndexofLeftParent\tIndexOfRightParent\tNameOfLeftParent\tNameOfRightParent\tDistanceToBestMatch\tcIndex\t(cIndex - singleDist)\tloonIndex\tMismatchesToChimera\tMismatchToTrimera\tChimeraBreakPoint\tLogisticProbability\tTypeOfSequence\n";
199 vector<bool> chimeras(numSeqs, 0);
201 for(int j=0;j<numSeqs;j++){
203 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; }
205 vector<bool> restricted = chimeras;
207 vector<vector<int> > leftDiffs(numSeqs);
208 vector<vector<int> > leftMaps(numSeqs);
209 vector<vector<int> > rightDiffs(numSeqs);
210 vector<vector<int> > rightMaps(numSeqs);
212 vector<int> singleLeft, bestLeft;
213 vector<int> singleRight, bestRight;
215 int bestSingleIndex, bestSingleDiff;
216 vector<pwAlign> alignments(numSeqs);
218 int comparisons = myPerseus.getAlignments(j, sequences, alignments, leftDiffs, leftMaps, rightDiffs, rightMaps, bestSingleIndex, bestSingleDiff, restricted);
220 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; }
222 int minMismatchToChimera, leftParentBi, rightParentBi, breakPointBi;
224 string dummyA, dummyB;
226 if(comparisons >= 2){
227 minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
229 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; }
231 int minMismatchToTrimera = numeric_limits<int>::max();
232 int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
234 if(minMismatchToChimera >= 3 && comparisons >= 3){
235 minMismatchToTrimera = myPerseus.getTrimera(sequences, leftDiffs, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight, restricted);
237 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; }
240 double singleDist = myPerseus.modeledPairwiseAlignSeqs(sequences[j].sequence, sequences[bestSingleIndex].sequence, dummyA, dummyB, correctModel);
242 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; }
245 string chimeraRefSeq;
247 if(minMismatchToChimera - minMismatchToTrimera >= 3){
249 chimeraRefSeq = myPerseus.stitchTrimera(alignments, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, leftMaps, rightMaps);
253 chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, leftMaps, rightMaps);
256 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; }
258 double chimeraDist = myPerseus.modeledPairwiseAlignSeqs(sequences[j].sequence, chimeraRefSeq, dummyA, dummyB, correctModel);
260 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; }
262 double cIndex = chimeraDist;//modeledPairwiseAlignSeqs(sequences[j].sequence, chimeraRefSeq);
263 double loonIndex = myPerseus.calcLoonIndex(sequences[j].sequence, sequences[leftParentBi].sequence, sequences[rightParentBi].sequence, breakPointBi, binMatrix);
265 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; }
267 chimeraFile << j << '\t' << sequences[j].seqName << '\t' << bestSingleDiff << '\t' << bestSingleIndex << '\t' << sequences[bestSingleIndex].seqName << '\t';
268 chimeraFile << minMismatchToChimera << '\t' << leftParentBi << '\t' << rightParentBi << '\t' << sequences[leftParentBi].seqName << '\t' << sequences[rightParentBi].seqName << '\t';
269 chimeraFile << singleDist << '\t' << cIndex << '\t' << (cIndex - singleDist) << '\t' << loonIndex << '\t';
270 chimeraFile << minMismatchToChimera << '\t' << minMismatchToTrimera << '\t' << breakPointBi << '\t';
272 double probability = myPerseus.classifyChimera(singleDist, cIndex, loonIndex, pDataArray->alpha, pDataArray->beta);
274 chimeraFile << probability << '\t';
276 if(probability > pDataArray->cutoff){
277 chimeraFile << type << endl;
278 accnosFile << sequences[j].seqName << endl;
283 chimeraFile << "good" << endl;
288 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;
291 if((j+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(j+1) + "\n"); }
294 if((numSeqs) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n"); }
298 ////////////////////////////////////////////////////////////////////////////////////////
300 totalSeqs += numSeqs;
303 pDataArray->m->appendFiles(chimeraFileName, pDataArray->outputFName); pDataArray->m->mothurRemove(chimeraFileName);
304 pDataArray->m->appendFiles(accnosFileName, pDataArray->accnos); pDataArray->m->mothurRemove(accnosFileName);
305 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();
307 if (pDataArray->m->control_pressed) { delete parser; pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
310 pDataArray->count = totalSeqs;
315 catch(exception& e) {
316 pDataArray->m->errorOut(e, "ChimeraUchimeCommand", "MyPerseusThreadFunction");
320 /**************************************************************************************************/