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// ==========================================================================
// Mason - A Read Simulator
// ==========================================================================
// 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Simulate a random genome.
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>
#include "simulate_genome.h"
// ==========================================================================
// Classes
// ==========================================================================
// --------------------------------------------------------------------------
// Class MasonGenomeOptions
// --------------------------------------------------------------------------
// This struct stores the options from the command line.
//
// You might want to rename this to reflect the name of your app.
struct MasonGenomeOptions
{
// Verbosity level. 0 -- quiet, 1 -- normal, 2 -- verbose, 3 -- very verbose.
int verbosity;
// The output file name.
seqan2::CharString outputFilename;
// Lengths of the contigs.
seqan2::String<int64_t> contigLengths;
// The seed to use for the RNG.
uint64_t seed;
MasonGenomeOptions() : verbosity(1), seed(0)
{}
};
// ==========================================================================
// Functions
// ==========================================================================
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
seqan2::ArgumentParser::ParseResult
parseCommandLine(MasonGenomeOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
seqan2::ArgumentParser parser("mason_genome");
// Set short description, version, and date.
setShortDescription(parser, "Random Genome Simulation");
setDateAndVersion(parser);
setCategory(parser, "Simulators");
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] [\\fB-l\\fP \\fILEN\\fP]+ \\fB-o\\fP \\fIOUT.fa\\fP");
addDescription(parser,
"Simulate a random genome to the output file. For each \\fB-l\\fP/\\fB--contig-length\\fP "
"entry, a contig with the given length will be simulated.");
// We require one argument.
addOption(parser, seqan2::ArgParseOption("q", "quiet", "Set verbosity to a minimum."));
addOption(parser, seqan2::ArgParseOption("v", "verbose", "Enable verbose output."));
addOption(parser, seqan2::ArgParseOption("vv", "very-verbose", "Enable very verbose output."));
addSection(parser, "Simulation Configuration");
addOption(parser, seqan2::ArgParseOption("l", "contig-length",
"Length of the contig to simulate. Give one \\fB-l\\fP "
"value for each contig to simulate.",
seqan2::ArgParseOption::INT64, "LENGTH", true));
setMinValue(parser, "contig-length", "1");
setRequired(parser, "contig-length");
addOption(parser, seqan2::ArgParseOption("s", "seed", "The seed to use for the random number generator.",
seqan2::ArgParseOption::INTEGER, "INT"));
setDefaultValue(parser, "seed", 42);
addSection(parser, "Output Options");
addOption(parser, seqan2::ArgParseOption("o", "out-file", "Output file.",
seqan2::ArgParseOption::OUTPUT_FILE, "FILE"));
setValidValues(parser, "out-file", seqan2::SeqFileOut::getFileExtensions());
setRequired(parser, "out-file");
// Add Examples Section.
addTextSection(parser, "Examples");
addListItem(parser, "\\fBmason_genome\\fP \\fB-l\\fP 1000 \\fB-l\\fP 4000 \\fB-o\\fP \\fIgenome.fa\\fP",
"Simulate a genome with two contigs of lengths 1000 and 4000 and write it to genome.fa.");
// Parse command line.
seqan2::ArgumentParser::ParseResult res = seqan2::parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != seqan2::ArgumentParser::PARSE_OK)
return res;
// 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;
getOptionValue(options.outputFilename, parser, "out-file");
getOptionValue(options.seed, parser, "seed");
for (unsigned i = 0; i < getOptionValueCount(parser, "contig-length"); ++i)
{
int64_t len = 0;
getOptionValue(len, parser, "contig-length", i);
appendValue(options.contigLengths, len);
}
return seqan2::ArgumentParser::PARSE_OK;
}
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
seqan2::ArgumentParser parser;
MasonGenomeOptions options;
seqan2::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 != seqan2::ArgumentParser::PARSE_OK)
return res == seqan2::ArgumentParser::PARSE_ERROR;
std::cout << "MASON GENOME SIMULATOR\n"
<< "======================\n\n";
// Print the command line arguments back to the user.
if (options.verbosity > 0)
{
std::cout << "__OPTIONS____________________________________________________________________\n"
<< '\n'
<< "VERBOSITY \t" << options.verbosity << '\n'
<< "\n"
<< "SEED \t" << options.seed << '\n'
<< "\n"
<< "OUTPUT FILE\t" << options.outputFilename << "\n"
<< "CONTIG LENS\t";
for (unsigned i = 0; i < length(options.contigLengths); ++i)
{
if (i > 0)
std::cout << ", ";
std::cout << options.contigLengths[i];
};
std::cout << "\n\n";
}
// Perform genome simulation.
std::cout << "__SIMULATING GENOME__________________________________________________________\n"
<< "\n";
MasonSimulateGenomeOptions simOptions;
simOptions.contigLengths = options.contigLengths;
simOptions.seed = options.seed;
if (simulateGenome(toCString(options.outputFilename), simOptions) != 0)
return 1;
std::cerr << "\nDone.\n";
return 0;
}
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