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// ==========================================================================
// four2three
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Sabrina Krakau <sabrina.krakau@fu-berlin.de>
// ==========================================================================
#include <iostream>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>
#include <seqan/arg_parse.h>
#include "four2three.h"
using namespace std;
using namespace seqan2;
struct AppOptions
{
// Verbosity level. 0 -- quiet, 1 -- normal, 2 -- verbose, 3 -- very verbose.
int verbosity;
CharString inputFileName;
bool ctConversion;
CharString outputFileName;
AppOptions() :
verbosity(1),
ctConversion(true)
{}
};
ArgumentParser::ParseResult
parseCommandLine(AppOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
ArgumentParser parser("four2three");
// Set short description, version, and date.
setShortDescription(parser, "Four to three-letter alphabet reduction.");
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
setDate(parser, SEQAN_DATE);
setCategory(parser, "BS-Seq Analysis");
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \"\\fISEQUENCE FILE\\fP\"");
addDescription(parser, "This program converts four-letter sequences into three-letter sequences for bisulfite sequence analysis.");
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "SEQUENCES"));
setHelpText(parser, 0, "A sequence file containing reads or genome.");
setValidValues(parser, 0, SeqFileIn::getFileExtensions());
addOption(parser, ArgParseOption("o", "output-file", "Name of output file.", ArgParseArgument::OUTPUT_FILE));
setValidValues(parser, "o", SeqFileOut::getFileExtensions());
setRequired(parser, "output-file", true);
addOption(parser, ArgParseOption("ga", "ga-conversion", "Convert Gs to As, instead of Cs to Ts."));
addOption(parser, ArgParseOption("q", "quiet", "Set verbosity to a minimum."));
addOption(parser, ArgParseOption("v", "verbose", "Enable verbose output."));
addOption(parser, ArgParseOption("vv", "very-verbose", "Enable very verbose output."));
// Add Examples Section.
addTextSection(parser, "Examples");
addListItem(parser, "\\fBfour2three\\fP \\fB-o\\fP \\fBreads_CT.fastq\\fP \\fBreads.fastq\\fP ",
"Converts sequences into three-letter alphabet by converting Cs to Ts.");
addListItem(parser, "\\fBfour2three\\fP \\fB-ga\\fP \\fB-o\\fP \\fBgenome_GA.fa\\fP \\fBgenome.fa\\fP ",
"Converts sequences into three-letter alphabet by converting Gs to As.");
// Parse command line.
ArgumentParser::ParseResult res = parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != ArgumentParser::PARSE_OK)
return res;
getArgumentValue(options.inputFileName, parser, 0);
getOptionValue(options.outputFileName, parser, "output-file");
if (isSet(parser, "ga-conversion"))
options.ctConversion = false;
CharString tmp1 = options.inputFileName;
toLower(tmp1);
CharString tmp2 = options.outputFileName;
toLower(tmp2);
if ( ( (endsWith(tmp1, ".fa") || endsWith(tmp1, ".fasta")) && (endsWith(tmp2, ".fastq") || endsWith(tmp2, ".fq")) ) ||
( (endsWith(tmp2, ".fa") || endsWith(tmp2, ".fasta")) && (endsWith(tmp1, ".fastq") || endsWith(tmp2, ".fq")) ) )
{
std::cerr << "ERROR: Output file must have the same format as input file!" << std::endl;
return ArgumentParser::PARSE_ERROR;
}
// Extract option values.
if (isSet(parser, "quiet"))
options.verbosity = 0;
if (isSet(parser, "verbose"))
options.verbosity = 2;
if (isSet(parser, "very-verbose"))
options.verbosity = 3;
return ArgumentParser::PARSE_OK;
}
int main(int argc, char const ** argv)
{
// Parse the command line.
ArgumentParser parser;
AppOptions options;
ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
if (res != ArgumentParser::PARSE_OK)
return res == ArgumentParser::PARSE_ERROR;
preProcess(options);
return 0;
}
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