1 #ifndef CLASSIFYOTUSCOMMAND_H
2 #define CLASSIFYOTUSCOMMAND_H
8 * Created by westcott on 6/1/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "listvector.hpp"
15 #include "inputdata.h"
18 class ClassifyOtuCommand : public Command {
21 ClassifyOtuCommand(string);
23 ~ClassifyOtuCommand() {}
25 vector<string> setParameters();
26 string getCommandName() { return "classify.otu"; }
27 string getCommandCategory() { return "Phylotype Analysis"; }
28 string getHelpString();
29 string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
30 string getDescription() { return "find the concensus taxonomy for each OTU"; }
33 void help() { m->mothurOut(getHelpString()); }
39 string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
40 bool abort, allLines, probs;
42 set<string> labels; //holds labels to be used
43 vector<string> outputNames;
44 map<string, string> nameMap;
45 map<string, string> taxMap;
48 int readTaxonomyFile();
49 void removeConfidences(string&);
50 int process(ListVector*);
51 vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin