+++ /dev/null
-#ifndef CLASSIFYSEQSCOMMAND_H
-#define CLASSIFYSEQSCOMMAND_H
-
-/*
- * classifyseqscommand.h
- * Mothur
- *
- * Created by westcott on 11/2/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "command.hpp"
-#include "classify.h"
-#include "referencedb.h"
-#include "sequence.hpp"
-#include "bayesian.h"
-#include "phylotree.h"
-#include "phylosummary.h"
-#include "knn.h"
-
-
-//KNN and Bayesian methods modeled from algorithms in
-//Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences
-//into the New Bacterial Taxonomy†
-//Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1*
-//Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University,
-//East Lansing, Michigan 48824
-//Received 10 January 2007/Accepted 18 June 2007
-
-
-
-class ClassifySeqsCommand : public Command {
-
-public:
- ClassifySeqsCommand(string);
- ClassifySeqsCommand();
- ~ClassifySeqsCommand();
-
- vector<string> setParameters();
- string getCommandName() { return "classify.seqs"; }
- string getCommandCategory() { return "Phylotype Analysis"; }
- string getHelpString();
- string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
- string getDescription() { return "classify sequences"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-
-
-private:
- struct linePair {
- unsigned long long start;
- unsigned long long end;
- linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
- };
-
- vector<int> processIDS; //processid
- vector<linePair*> lines;
- vector<string> fastaFileNames;
- vector<string> namefileNames;
- vector<string> groupfileNames;
- vector<string> outputNames;
- map<string, vector<string> > nameMap;
- map<string, vector<string> >::iterator itNames;
-
- Classify* classify;
- ReferenceDB* rdb;
-
- string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
- int processors, kmerSize, numWanted, cutoff, iters;
- float match, misMatch, gapOpen, gapExtend;
- bool abort, probs, save, flip;
-
- int driver(linePair*, string, string, string, string);
- void appendTaxFiles(string, string);
- int createProcesses(string, string, string, string);
- string addUnclassifieds(string, int);
-
- int MPIReadNamesFile(string);
- #ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
- #endif
-};
-
-/**************************************************************************************************/
-//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 classifyData {
- string taxFName;
- string tempTFName;
- string filename;
- string search, taxonomyFileName, templateFileName, method, accnos;
- unsigned long long start;
- unsigned long long end;
- MothurOut* m;
- float match, misMatch, gapOpen, gapExtend;
- int count, kmerSize, threadID, cutoff, iters, numWanted;
- bool probs, flip;
-
- classifyData(){}
- classifyData(string acc, bool p, string me, string te, string tx, string a, string r, string f, string se, int ks, int i, int numW, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int cut, int tid, bool fli) {
- accnos = acc;
- taxonomyFileName = tx;
- templateFileName = te;
- taxFName = a;
- tempTFName = r;
- filename = f;
- search = se;
- method = me;
- m = mout;
- start = st;
- end = en;
- match = ma;
- misMatch = misMa;
- gapOpen = gapO;
- gapExtend = gapE;
- kmerSize = ks;
- cutoff = cut;
- iters = i;
- numWanted = numW;
- threadID = tid;
- probs = p;
- count = 0;
- flip = fli;
- }
-};
-
-/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
-static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
- classifyData* pDataArray;
- pDataArray = (classifyData*)lpParam;
-
- try {
- ofstream outTax;
- pDataArray->m->openOutputFile(pDataArray->taxFName, outTax);
-
- ofstream outTaxSimple;
- pDataArray->m->openOutputFile(pDataArray->tempTFName, outTaxSimple);
-
- ofstream outAcc;
- pDataArray->m->openOutputFile(pDataArray->accnos, outAcc);
-
- ifstream inFASTA;
- pDataArray->m->openInputFile(pDataArray->filename, inFASTA);
-
- string taxonomy;
-
- //print header if you are process 0
- if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
- inFASTA.seekg(0);
- }else { //this accounts for the difference in line endings.
- inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA);
- }
-
- pDataArray->count = pDataArray->end;
-
- //make classify
- Classify* myclassify;
- if(pDataArray->method == "bayesian"){ myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID, pDataArray->flip); }
- else if(pDataArray->method == "knn"){ myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID); }
- else {
- pDataArray->m->mothurOut(pDataArray->search + " is not a valid method option. I will run the command using bayesian.");
- pDataArray->m->mothurOutEndLine();
- myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID, pDataArray->flip);
- }
-
- if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
-
- int count = 0;
- for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
-
- if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
-
- Sequence* candidateSeq = new Sequence(inFASTA); pDataArray->m->gobble(inFASTA);
-
- if (candidateSeq->getName() != "") {
-
- taxonomy = myclassify->getTaxonomy(candidateSeq);
-
- if (pDataArray->m->control_pressed) { delete candidateSeq; return 0; }
-
- if (taxonomy == "unknown;") { pDataArray->m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); pDataArray->m->mothurOutEndLine(); }
-
- //output confidence scores or not
- if (pDataArray->probs) {
- outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
- }else{
- outTax << candidateSeq->getName() << '\t' << myclassify->getSimpleTax() << endl;
- }
-
- outTaxSimple << candidateSeq->getName() << '\t' << myclassify->getSimpleTax() << endl;
-
- if (myclassify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
-
- count++;
- }
- delete candidateSeq;
- //report progress
- if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
-
- }
- //report progress
- if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
-
- delete myclassify;
- inFASTA.close();
- outTax.close();
- outTaxSimple.close();
-
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "ClassifySeqsCommand", "MyClassThreadFunction");
- exit(1);
- }
-}
-#endif
-
-
-
-
-#endif
-
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