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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
|
/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
==========================================================================*/
#include <seqan/basic.h>
#include <seqan/graph_msa.h>
#include <seqan/modifier.h>
#include <seqan/misc/misc_cmdparser.h>
#include <iostream>
#include <fstream>
using namespace seqan;
//////////////////////////////////////////////////////////////////////////////////
inline void
_addVersion(CommandLineParser& parser) {
::std::string rev = "$Revision: 4692 $";
addVersionLine(parser, "Version 1.01 (18. August 2009) Revision: " + rev.substr(11, 4) + "");
}
//////////////////////////////////////////////////////////////////////////////////
template<typename TFile, typename TMat, typename TNames>
inline void
_readPhylipMatrix(TFile& file,
TMat& matrix,
TNames& names)
{
typedef typename Value<TFile>::Type TValue;
typedef typename Value<TMat>::Type TDistance;
typedef typename Size<TMat>::Type TSize;
typedef typename Value<TNames>::Type TName;
typedef typename Iterator<TMat, Standard>::Type TMatIter;
// Parse the file and convert the internal ids
TValue c;
if (_streamEOF(file)) return;
else c = _streamGet(file);
while (!_streamEOF(file)) {
if (_streamEOF(file)) break;
_parse_skipWhitespace(file, c);
TSize nseq = _parse_readNumber(file, c);
_parse_skipWhitespace(file, c);
resize(matrix, nseq * nseq);
resize(names, nseq);
TMatIter it = begin(matrix, Standard());
for(TSize row = 0; row<nseq; ++row) {
_parse_readIdentifier(file, names[row], c);
_parse_skipWhitespace(file, c);
for(TSize col = 0; col<nseq; ++col, ++it) {
*it = _parse_readDouble(file, c);
_parse_skipWhitespace(file, c);
}
}
}
}
//////////////////////////////////////////////////////////////////////////////////
int main(int argc, const char *argv[]) {
// Command line parsing
CommandLineParser parser;
_addVersion(parser);
addTitleLine(parser, "***************************************");
addTitleLine(parser, "* Tree reconstrucion - TreeRecon *");
addTitleLine(parser, "* (c) Copyright 2009 by Tobias Rausch *");
addTitleLine(parser, "***************************************");
addUsageLine(parser, "-m <Phylip distance matrix> [Options]");
addSection(parser, "Main Options:");
addOption(parser, addArgumentText(CommandLineOption("m", "matrix", "file with distance matrix", OptionType::String), "<Phylip distance matrix>"));
addHelpLine(parser, "At least 3 species required.");
addOption(parser, addArgumentText(CommandLineOption("b", "build", "tree building method", (int)OptionType::String, "nj"), "[nj, min, max, avg, wavg]"));
addHelpLine(parser, "nj = Neighbor-joining");
addHelpLine(parser, "min = UPGMA single linkage");
addHelpLine(parser, "max = UPGMA complete linkage");
addHelpLine(parser, "avg = UPGMA average linkage");
addHelpLine(parser, "wavg = UPGMA weighted average linkage");
addHelpLine(parser, "/*Neighbor-joining creates an");
addHelpLine(parser, " unrooted tree. We root that tree");
addHelpLine(parser, " at the last joined pair.*/");
addOption(parser, addArgumentText(CommandLineOption("o", "outfile", "output filename", (int)OptionType::String, "tree.dot"), "<Filename>"));
addOption(parser, addArgumentText(CommandLineOption("f", "format", "output format", (int)OptionType::String, "dot"), "[dot | newick]"));
if (argc == 1)
{
shortHelp(parser, std::cerr); // print short help and exit
return 0;
}
if (!parse(parser, argc, argv, ::std::cerr)) return 1;
if (isSetLong(parser, "help") || isSetLong(parser, "version")) return 0; // print help or version and exit
// Tree reconstruction
typedef double TDistanceValue;
typedef String<char> TName;
typedef Size<TName>::Type TSize;
// Read the options
::std::string infile;
getOptionValueLong(parser, "matrix", infile);
::std::string outfile;
getOptionValueLong(parser, "outfile", outfile);
TSize build = 0;
String<char> meth;
getOptionValueLong(parser, "build", meth);
if (meth == "nj") build = 0;
else if (meth == "min") build = 1;
else if (meth == "max") build = 2;
else if (meth == "avg") build = 3;
else if (meth == "wavg") build = 4;
String<char> format;
getOptionValueLong(parser, "format", format);
// Read the distance matrix
String<TName> names;
String<TDistanceValue> matrix;
FILE* strmMat = fopen(infile.c_str(), "rb");
_readPhylipMatrix(strmMat, matrix, names);
fclose(strmMat);
// Create the tree
Graph<Tree<TDistanceValue> > tree;
if (build == 0) njTree(matrix, tree);
else if (build == 1) upgmaTree(matrix, tree, UpgmaMin());
else if (build == 2) upgmaTree(matrix, tree, UpgmaMax());
else if (build == 3) upgmaTree(matrix, tree, UpgmaAvg());
else if (build == 4) upgmaTree(matrix, tree, UpgmaWeightAvg());
if (format == "dot") {
TSize nameLen = length(names);
resize(names, numVertices(tree));
// Add the label prefix for leaves
for(TSize i = 0;i < nameLen; ++i) {
TName tmpName = "label = \"";
append(tmpName, names[i], Generous());
append(tmpName, '"');
names[i] = tmpName;
}
// Append emty names for internal vertices
for(;nameLen < length(names); ++nameLen) {
names[nameLen] = "label = \"\"";
}
// Write the result
FILE* strmDot;
strmDot = fopen(outfile.c_str(), "w");
write(strmDot, tree, names, DotDrawing());
fclose(strmDot);
} else if (format == "newick") {
FILE* strmDot;
strmDot = fopen(outfile.c_str(), "w");
// If nj tree collapse the root
if (build == 0) write(strmDot, tree, names, true, NewickFormat());
else write(strmDot, tree, names, false, NewickFormat());
fclose(strmDot);
}
return 0;
}
|
