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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
// -----------------------------------------------------------------------------------------------------
#include <sstream>
#include <gtest/gtest.h>
#include <seqan3/io/sequence_file/output.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/range/views/persist.hpp>
#include <seqan3/range/views/take.hpp>
#include <seqan3/test/tmp_filename.hpp>
#include <seqan3/std/iterator>
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(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"
};
#if !SEQAN3_WORKAROUND_GCC_93983
// valid without assignment?
seqan3::sequence_file_input{std::istringstream{input},
seqan3::format_fasta{}} | seqan3::views::persist
| seqan3::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{}}
| seqan3::views::persist
| seqan3::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);
#endif // !SEQAN3_WORKAROUND_GCC_93983
}
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);
}
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