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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#if __has_include(<seqan/seq_io.h>)
#include <seqan/seq_io.h>
#endif
#include <algorithm>
#include <cctype>
#include <cstring>
#include <benchmark/benchmark.h>
#include <range/v3/algorithm/equal.hpp>
#include <range/v3/view/transform.hpp>
#include <seqan3/alphabet/quality/all.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/io/sequence_file/format_fasta.hpp>
#include <seqan3/range/views/convert.hpp>
#include <seqan3/test/performance/units.hpp>
#include <sstream>
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 write3(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(write3);
#if __has_include(<seqan/seq_io.h>)
void write2(benchmark::State & state)
{
std::ostringstream ostream;
seqan::CharString id = fasta_hdr;
seqan::Dna5String seq = fasta_seq;
for (auto _ : state)
{
for (size_t i = 0; i < iterations_per_run; ++i)
seqan::writeRecord(ostream, id, seq, seqan::Fasta());
}
ostream = std::ostringstream{};
seqan::writeRecord(ostream, id, seq, seqan::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(write2);
#endif
void read3(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(read3);
#if __has_include(<seqan/seq_io.h>)
#include <fstream>
void read2(benchmark::State & state)
{
seqan::CharString id;
seqan::Dna5String seq;
std::istringstream istream{fasta_file};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = seqan::Iter<std::istringstream, seqan::StreamIterator<seqan::Input> >(istream);
for (size_t i = 0; i < iterations_per_run; ++i)
{
readRecord(id, seq, it, seqan::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(read2);
#endif
BENCHMARK_MAIN();
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