makebiomcommand.h

   1 #ifndef Mothur_makebiomcommand_h
   2 #define Mothur_makebiomcommand_h
   3
   4 //
   5 //  makebiomcommand.h
   6 //  Mothur
   7 //
   8 //  Created by Sarah Westcott on 4/16/12.
   9 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
  10 //
  11
  12
  13 #include "command.hpp"
  14 #include "sharedrabundvector.h"
  15 #include "inputdata.h"
  16
  17
  18 class MakeBiomCommand : public Command {
  19
  20 public:
  21         MakeBiomCommand(string);
  22         MakeBiomCommand();
  23         ~MakeBiomCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "make.biom";   }
  27         string getCommandCategory()             { return "General";             }
  28
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
  32         string getDescription()         { return "creates a biom file"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38
  39         string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax, picrustOtuFile;
  40         vector<string> outputNames, Groups, sampleMetadata;
  41         set<string> labels;
  42
  43         bool abort, allLines, picrust;
  44
  45     int getBiom(vector<SharedRAbundVector*>&);
  46     vector<string> getMetaData(vector<SharedRAbundVector*>&);
  47     vector<string> parseTax(string tax, vector<string>& scores);
  48     int getSampleMetaData(vector<SharedRAbundVector*>&);
  49     //for picrust
  50     int getGreenGenesOTUIDs(vector<SharedRAbundVector*>&, map<string, string>&);
  51     map<string, string> readGGOtuMap();
  52 };
  53
  54
  55 #endif