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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#if __has_include(<seqan/seq_io.h>)
# include <seqan/seq_io.h>
#endif
#include <benchmark/benchmark.h>
#include <algorithm>
#include <cctype>
#include <cstring>
#include <sstream>
#include <seqan3/alphabet/quality/all.hpp>
#include <seqan3/io/sequence_file/format_fasta.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/io/sequence_file/input_format_concept.hpp>
#include <seqan3/io/sequence_file/output.hpp>
#include <seqan3/io/sequence_file/output_format_concept.hpp>
#include <seqan3/test/performance/units.hpp>
#include <seqan3/utility/views/convert.hpp>
inline constexpr size_t iterations_per_run = 1024;
inline std::string const fasta_hdr{"seq foobar blobber"};
inline std::string const fasta_seq{"ACTAGACTAGCTACGATCAGCTACGATCAGCTACGAACTAGACTAGCTACGATACTAGACTAGCTACGATCAGCTACGA"
"ACTAGACTAGCTACGATCAGCTACGATCAGCTACGAACTAGACTAGCTACGATACTAGACTAGCTACGATCAGCTACGA"
"ACTAGACTAGCTACGATCAGCTACGATCAGCTACGAACTAGACTAGCTACGATACTAGACTAGCTACGATCAGCTACGA"
"ACTAGACTAGCTACGATCAGCTACGATCAGCTACGAACTAGACTAGCTACGATACTAGACTAGCTACGATCAGCTACGA"
"ACTAGACTAGCTACGATCAGCTACGATCAGCTACGAACTAGACTAGCTACGATACTAGACTAGCTACGATCAGCTACGA"
"ACTAGACTAGCTACGATCAGCTACGATCAGCTACGAACTAGACTAGCTACGATACTAGACTAGCTACGATCAGCTACGA"};
//TODO: benchmark with spaces/newlines
static std::string fasta_file = []()
{
std::string file{};
for (size_t idx = 0; idx < iterations_per_run; idx++)
file += "> " + fasta_hdr + "\n" + fasta_seq + "\n";
return file;
}();
void seqan3_dna5_ostringstream_write(benchmark::State & state)
{
std::ostringstream ostream;
seqan3::sequence_file_output fout{ostream,
seqan3::format_fasta{},
seqan3::fields<seqan3::field::id, seqan3::field::seq>{}};
for (auto _ : state)
{
for (size_t i = 0; i < iterations_per_run; ++i)
fout.emplace_back(fasta_seq, fasta_hdr);
}
ostream = std::ostringstream{};
fout.emplace_back(fasta_seq, fasta_hdr);
size_t bytes_per_run = ostream.str().size() * iterations_per_run;
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(seqan3_dna5_ostringstream_write);
#if __has_include(<seqan/seq_io.h>)
void seqan2_dna5_ostringstream_write(benchmark::State & state)
{
std::ostringstream ostream;
seqan2::CharString id = fasta_hdr;
seqan2::Dna5String seq = fasta_seq;
for (auto _ : state)
{
for (size_t i = 0; i < iterations_per_run; ++i)
seqan2::writeRecord(ostream, id, seq, seqan2::Fasta());
}
ostream = std::ostringstream{};
seqan2::writeRecord(ostream, id, seq, seqan2::Fasta());
size_t bytes_per_run = ostream.str().size() * iterations_per_run;
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(seqan2_dna5_ostringstream_write);
#endif
void seqan3_dna5_istringstream_read(benchmark::State & state)
{
std::istringstream istream{fasta_file};
seqan3::sequence_file_input fin{istream, seqan3::format_fasta{}};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = fin.begin();
for (size_t i = 0; i < iterations_per_run; ++i)
it++;
}
size_t bytes_per_run = fasta_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(seqan3_dna5_istringstream_read);
#if __has_include(<seqan/seq_io.h>)
# include <fstream>
void seqan2_dna5_istringstream_read(benchmark::State & state)
{
seqan2::CharString id;
seqan2::Dna5String seq;
std::istringstream istream{fasta_file};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = seqan2::Iter<std::istringstream, seqan2::StreamIterator<seqan2::Input>>(istream);
for (size_t i = 0; i < iterations_per_run; ++i)
{
readRecord(id, seq, it, seqan2::Fasta{});
clear(id);
clear(seq);
}
}
size_t bytes_per_run = fasta_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(seqan2_dna5_istringstream_read);
#endif
BENCHMARK_MAIN();
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