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/*==========================================================================
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;
}
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