1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
#ifndef GETOTUREPCOMMAND_H
#define GETOTUREPCOMMAND_H
/*
* getoturepcommand.h
* Mothur
*
* Created by Sarah Westcott on 4/6/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
/* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
#include "fastamap.h"
#include "groupmap.h"
#include "counttable.h"
#include "optimatrix.h"
#include "nameassignment.hpp"
#include "countseqscommand.h"
#include "getseqscommand.h"
#include "calculator.h"
#include "mcc.hpp"
typedef map<int, float> SeqMap;
struct repStruct {
string name;
string sequence;
string bin;
int simpleBin;
int size;
string group;
repStruct(){}
repStruct(string n, string seq, string b, int sb, int s, string g) : name(n), bin(b), size(s), group(g), simpleBin(sb), sequence(seq) { }
~repStruct() = default;
};
class GetOTURepCommand : public Command {
public:
GetOTURepCommand(string);
~GetOTURepCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.oturep"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
string getDescription() { return "gets a representative sequence for each OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
map<string, int> nameMap;
OptiData* matrix;
CountTable ct;
string filename, fastafile, listfile, namefile, groupfile, sorted, phylipfile, countfile, columnfile, distFile, format, groups, method;
ofstream out;
ifstream in, inNames, inRow;
bool abort, allLines, groupError, weighted, hasGroups, rename, cutoffSet;
vector<string> outputNames, Groups;
map<string, string> outputNameFiles;
set<string> cutoffs;
float cutoff;
int precision;
void readNamesFile(FastaMap&);
int process(ListVector*, GroupMap&);
string findRep(vector<string>, map<string, long long>&, string); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
string findRepAbund(vector<string>, string);
int processNames(string, string);
int processFastaNames(string, string, FastaMap&, GroupMap&);
int readDist();
void createCount();
};
#endif
|
