1 #ifndef DECONVOLUTECOMMAND_H 2 #define DECONVOLUTECOMMAND_H 3 /* 4 * deconvolute.h 5 * Mothur 6 * 7 * Created by Sarah Westcott on 1/21/09. 8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. 9 * 10 */ 11 12 #include "command.hpp" 13 #include "fastamap.h" 14 #include "counttable.h" 15 16 /* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file 17 containing 2 columns. The first being the groupname and the second the list of identical sequence names. */ 18 19 20 class DeconvoluteCommand : public Command { 21 22 public: 23 DeconvoluteCommand(string); ~DeconvoluteCommand()24 ~DeconvoluteCommand() {} 25 26 vector<string> setParameters(); getCommandName()27 string getCommandName() { return "unique.seqs"; } getCommandCategory()28 string getCommandCategory() { return "Sequence Processing"; } 29 30 string getHelpString(); 31 string getOutputPattern(string); getCitation()32 string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; } getDescription()33 string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; } 34 35 36 int execute(); help()37 void help() { m->mothurOut(getHelpString()); } 38 39 40 private: 41 string fastafile, namefile, countfile, format; 42 vector<string> outputNames; 43 44 bool abort; 45 }; 46 47 #endif 48