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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
|
/*==========================================================================
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/consensus.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: 4663 $";
addVersionLine(parser, "Version 0.22 (06. August 2009) Revision: " + rev.substr(11, 4) + "");
}
//////////////////////////////////////////////////////////////////////////////////
int main(int argc, const char *argv[]) {
// Command line parsing
CommandLineParser parser;
_addVersion(parser);
addTitleLine(parser, "***************************************");
addTitleLine(parser, "* Multi-read alignment - SeqCons *");
addTitleLine(parser, "* (c) Copyright 2009 by Tobias Rausch *");
addTitleLine(parser, "***************************************");
addUsageLine(parser, "-r <FASTA file with reads> [Options]");
addUsageLine(parser, "-a <AMOS message file> [Options]");
addSection(parser, "Main Options:");
addOption(parser, addArgumentText(CommandLineOption("r", "reads", "file with reads", OptionType::String), "<FASTA reads file>"));
addOption(parser, addArgumentText(CommandLineOption("a", "afg", "message file", OptionType::String), "<AMOS afg file>"));
addOption(parser, addArgumentText(CommandLineOption("o", "outfile", "output filename", (int)OptionType::String, "align.txt"), "<Filename>"));
addOption(parser, addArgumentText(CommandLineOption("f", "format", "output format", (int)OptionType::String, "afg"), "[seqan | afg]"));
addOption(parser, addArgumentText(CommandLineOption("m", "method", "alignment method", (int)OptionType::String, "realign"), "[realign | msa]"));
addOption(parser, addArgumentText(CommandLineOption("b", "bandwidth", "bandwidth", (int)OptionType::Int, 8), "<Int>"));
addOption(parser, CommandLineOption("n", "noalign", "no align, only convert input", OptionType::Boolean));
addSection(parser, "MSA Method Options:");
addOption(parser, addArgumentText(CommandLineOption("ma", "matchlength", "min. overlap length", (int)OptionType::Int, 15), "<Int>"));
addOption(parser, addArgumentText(CommandLineOption("qu", "quality", "min. overlap precent identity", (int)OptionType::Int, 80), "<Int>"));
addOption(parser, addArgumentText(CommandLineOption("ov", "overlaps", "min. number of overlaps per read", (int)OptionType::Int, 3), "<Int>"));
addOption(parser, addArgumentText(CommandLineOption("wi", "window", "window size", (int)OptionType::Int, 0), "<Int>"));
addHelpLine(parser, "/*If this parameter is > 0 then all");
addHelpLine(parser, " overlaps within a given window");
addHelpLine(parser, " are computed.*/");
addSection(parser, "ReAlign Method Options:");
addOption(parser, CommandLineOption("in", "include", "include contig sequence", OptionType::Boolean));
addOption(parser, addArgumentText(CommandLineOption("rm", "rmethod", "realign method", (int)OptionType::String, "gotoh"), "[nw | gotoh]"));
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
// Get all command line options
ConsensusOptions consOpt;
// Main options
getOptionValueLong(parser, "reads", consOpt.readsfile);
getOptionValueLong(parser, "afg", consOpt.afgfile);
getOptionValueLong(parser, "outfile", consOpt.outfile);
String<char> optionVal;
getOptionValueLong(parser, "format", optionVal);
if (optionVal == "seqan") consOpt.output = 0;
else if (optionVal == "afg") consOpt.output = 1;
else if (optionVal == "frg") consOpt.output = 2;
else if (optionVal == "cgb") consOpt.output = 3;
getOptionValueLong(parser, "method", optionVal);
if (optionVal == "realign") consOpt.method = 0;
else if (optionVal == "msa") consOpt.method = 1;
getOptionValueLong(parser, "bandwidth", consOpt.bandwidth);
#ifdef CELERA_OFFSET
if (!isSetLong(parser, "bandwidth")) consOpt.bandwidth = 15;
#endif
getOptionValueLong(parser, "noalign", consOpt.noalign);
// Msa options
getOptionValueLong(parser, "matchlength", consOpt.matchlength);
getOptionValueLong(parser, "quality", consOpt.quality);
getOptionValueLong(parser, "overlaps", consOpt.overlaps);
#ifdef CELERA_OFFSET
if (!isSetLong(parser, "overlaps")) consOpt.overlaps = 5;
#endif
getOptionValueLong(parser, "window", consOpt.window);
// ReAlign options
getOptionValueLong(parser, "include", consOpt.include);
getOptionValueLong(parser, "rmethod", optionVal);
if (optionVal == "nw") consOpt.rmethod = 0;
else if (optionVal == "gotoh") consOpt.rmethod = 1;
// Create a new fragment store
typedef FragmentStore<> TFragmentStore;
typedef Size<TFragmentStore>::Type TSize;
TFragmentStore fragStore;
// Load the reads and layout positions
TSize numberOfContigs = 0;
if (!empty(consOpt.readsfile)) {
// Load simple read file
FILE* strmReads = fopen(consOpt.readsfile.c_str(), "rb");
bool moveToFront = false;
if (consOpt.noalign) moveToFront = true;
bool success = _convertSimpleReadFile(strmReads, fragStore, consOpt.readsfile, moveToFront);
fclose(strmReads);
if (!success) {
shortHelp(parser, std::cerr);
return 0;
}
numberOfContigs = 1;
} else if (!empty(consOpt.afgfile)) {
// Load Amos message file
FILE* strmReads = fopen(consOpt.afgfile.c_str(), "rb");
read(strmReads, fragStore, Amos());
fclose(strmReads);
numberOfContigs = length(fragStore.contigStore);
} else {
shortHelp(parser, std::cerr);
return 0;
}
// Multi-realignment desired or just conversion of the input
if (!consOpt.noalign) {
// Iterate over all contigs
for(TSize currentContig = 0; currentContig < numberOfContigs; ++currentContig) {
if (consOpt.method == 0) {
Score<int, WeightedConsensusScore<Score<int, FractionalScore>, Score<int, ConsensusScore> > > combinedScore;
reAlign(fragStore, combinedScore, currentContig, consOpt.rmethod, consOpt.bandwidth, consOpt.include);
} else {
// Import all reads of the given contig
typedef TFragmentStore::TReadSeq TReadSeq;
StringSet<TReadSeq, Owner<> > readSet;
String<Pair<TSize, TSize> > begEndPos;
_loadContigReads(readSet, begEndPos, fragStore, currentContig);
if (!length(readSet)) continue;
// Align the reads
typedef StringSet<TReadSeq, Dependent<> > TStringSet;
typedef Graph<Alignment<TStringSet, void, WithoutEdgeId> > TAlignGraph;
TAlignGraph gOut(readSet);
consensusAlignment(gOut, begEndPos, consOpt);
// Update the contig in the fragment store
updateContig(fragStore, gOut, currentContig);
clear(gOut);
//// Debug code for CA
//mtRandInit();
//String<char> fileTmp1 = "tmp1";
//String<char> fileTmp2 = "tmp2";
//for(int i = 0; i<10; ++i) {
// int file = (mtRand() % 20) + 65;
// appendValue(fileTmp1, char(file));
// appendValue(fileTmp2, char(file));
//}
//std::fstream strm3;
//strm3.open(toCString(fileTmp2), std::ios_base::out | std::ios_base::trunc);
//for(int i = 0;i<(int) length(origStrSet); ++i) {
// std::stringstream name;
// name << value(begEndPos, i).i1 << "," << value(begEndPos, i).i2;
// String<char> myTitle = name.str();
// write(strm3, origStrSet[i], myTitle, Fasta());
// if (value(begEndPos, i).i1 > value(begEndPos, i).i2) reverseComplementInPlace(origStrSet[i]);
//}
//strm3.close();
}
} // end loop over all contigs
}
// Output
if (consOpt.output == 0) {
// Write old SeqAn multi-read alignment format
FILE* strmWrite = fopen(consOpt.outfile.c_str(), "w");
write(strmWrite, fragStore, FastaReadFormat());
fclose(strmWrite);
} else if (consOpt.output == 1) {
// Write Amos
FILE* strmWrite = fopen(consOpt.outfile.c_str(), "w");
write(strmWrite, fragStore, Amos());
fclose(strmWrite);
} else if (consOpt.output == 2) {
FILE* strmWrite = fopen(consOpt.outfile.c_str(), "w");
_writeCeleraFrg(strmWrite, fragStore);
fclose(strmWrite);
} else if (consOpt.output == 3) {
FILE* strmWrite = fopen(consOpt.outfile.c_str(), "w");
_writeCeleraCgb(strmWrite, fragStore);
fclose(strmWrite);
}
return 0;
}
|
