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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
#include <gtest/gtest.h>
#include <iterator>
#include <sstream>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/io/sequence_file/output.hpp>
TEST(rows, assign_sequence_files)
{
std::string const input{
">TEST 1\n"
"ACGT\n"
">Test2\n"
"AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN\n\n"
">Test3\n"
"GGAGTATAATATATATATATATAT\n"};
std::string const output_comp{
">TEST 1\n"
"ACGT\n"
">Test2\n"
"AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
">Test3\n"
"GGAGTATAATATATATATATATAT\n"};
seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};
seqan3::sequence_file_output fout{std::ostringstream{}, seqan3::format_fasta{}};
fout.options.fasta_letters_per_line = 0;
fout = fin;
fout.get_stream().flush();
EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), output_comp);
}
TEST(rows, assign_sequence_files_read_blanks)
{
std::string const input{
">TEST 1\n"
"ACGT\n"
"> Test2\n"
"AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
"> Test3\n"
"GGAGTATAATATATATATATATAT\n"};
std::string const expected_output = input;
seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};
fin.options.fasta_ignore_blanks_before_id = false;
seqan3::sequence_file_output fout{std::ostringstream{}, seqan3::format_fasta{}};
fout.options.fasta_letters_per_line = 0;
fout = fin;
fout.get_stream().flush();
std::string const output = reinterpret_cast<std::ostringstream &>(fout.get_stream()).str();
EXPECT_EQ(output, expected_output);
}
TEST(integration, assign_sequence_file_pipes)
{
std::string const input{">TEST1\n"
"ACGT\n"
">Test2\n"
"AGGCTGNAGGCTGAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
">Test3\n"
"GGAGTATAATATATATATATATAT\n"};
// valid without assignment?
seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}}
| seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};
// valid with assignment and check contents
auto fout = seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}}
| seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};
fout.get_stream().flush();
EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), input);
}
TEST(integration, view)
{
std::string const input{">TEST1\n"
"ACGT\n"
">Test2\n"
"AGGCTGNAGGCTGAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
">Test3\n"
"GGAGTATAATATATATATATATAT\n"};
std::string const output{">TEST1\n"
"ACGT\n"
">Test2\n"
"AGGCTGNAGGCTGAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"};
// valid without assignment?
seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}} | std::views::all
| std::views::take(2) | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};
// valid with assignment and check contents
auto fout = seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}} | std::views::all
| std::views::take(2) | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};
fout.get_stream().flush();
EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), output);
}
TEST(integration, convert_fastq_to_fasta)
{
std::string const fastq_in{"@ID1\n"
"ACGTT\n"
"+\n"
"!##$%\n"
"@ID2\n"
"TATTA\n"
"+\n"
",BDEB\n"};
std::string const fasta_out{">ID1\n"
"ACGTT\n"
">ID2\n"
"TATTA\n"};
auto fout = seqan3::sequence_file_input{std::istringstream{fastq_in}, seqan3::format_fastq{}}
| seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};
fout.get_stream().flush();
EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), fasta_out);
}
TEST(integration, sequence_name_contains_id_tag)
{
// The sequence id is '>TEST 1'.
std::string const input{"> >TEST 1\n"
"ACGT\n"};
std::string const expected_output{">>TEST 1\n"
"ACGT\n"};
seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};
seqan3::sequence_file_output fout{std::ostringstream{}, seqan3::format_fasta{}};
fout = fin;
fout.get_stream().flush();
std::string const output = static_cast<std::ostringstream &>(fout.get_stream()).str();
EXPECT_EQ(output, expected_output);
}
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