#include "mothur.h"
#include "command.hpp"
-#include "alignment.hpp"
#include "classify.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(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"; }
+
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
struct linePair {
- int start;
- int numSeqs;
- linePair(int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int 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;
- string fastaFileName, templateFileName, distanceFileName, search, method, taxonomyFileName;
- int processors, kmerSize, numWanted;
+ string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
+ int processors, kmerSize, numWanted, cutoff, iters;
float match, misMatch, gapOpen, gapExtend;
- bool abort;
+ bool abort, probs;
- int driver(linePair*, string);
+ int driver(linePair*, string, string, string);
void appendTaxFiles(string, string);
- void createProcesses(string);
+ int createProcesses(string, string, string);
+ string addUnclassifieds(string, int);
+
+ int MPIReadNamesFile(string);
+ #ifdef USE_MPI
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ #endif
};
#endif