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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/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_embl.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/test/pretty_printing.hpp>
#include "sequence_file_format_test_template.hpp"
template <>
struct sequence_file_read<seqan3::format_embl> : public sequence_file_data
{
std::string standard_input
{
R"(ID ID1; stuff
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTT 18
//
ID ID2;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT 60
TTTTTTTTTT TTTTTTTTTT TT 82
//
ID ID3 lala;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTA 7
//)"
};
std::string illegal_alphabet_character_input
{
R"(ID ID1; stuff
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
AXGTTTTTTT TTTTTTTT 18
//)"
};
std::string standard_output
{
R"(ID ID1; 18 BP.
SQ Sequence 18 BP;
ACGTTTTTTT TTTTTTTT 18
//
ID ID2; 82 BP.
SQ Sequence 82 BP;
ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT 60
TTTTTTTTTT TTTTTTTTTT TT 82
//
ID ID3 lala; 7 BP.
SQ Sequence 7 BP;
ACGTTTA 7
//
)"
};
std::string no_or_ill_formatted_id_input
{
R"(IK ID1; stuff
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTT 18
//)"
};
};
// ---------------------------------------------------------------------------------------------------------------------
// parametrized tests
// ---------------------------------------------------------------------------------------------------------------------
INSTANTIATE_TYPED_TEST_SUITE_P(embl, sequence_file_read, seqan3::format_embl, );
INSTANTIATE_TYPED_TEST_SUITE_P(embl, sequence_file_write, seqan3::format_embl, );
// ----------------------------------------------------------------------------
// reading
// ----------------------------------------------------------------------------
struct read : public sequence_file_data
{
std::string input
{
R"(ID ID1; stuff
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTT 18
//
ID ID2;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT 60
TTTTTTTTTT TTTTTTTTTT TT 82
//
ID ID3 lala;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTA 7
//)"
};
seqan3::sequence_file_input_options<seqan3::dna15, false> options{};
void do_read_test(std::string const & input)
{
std::stringstream istream{input};
seqan3::sequence_file_input fin{istream, seqan3::format_embl{}, seqan3::fields<seqan3::field::id,
seqan3::field::seq>{}};
fin.options = options;
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, ++it)
{
EXPECT_EQ(seqan3::get<seqan3::field::id>(*it), ids[i]);
EXPECT_EQ(seqan3::get<seqan3::field::seq>(*it), seqs[i]);
}
}
};
TEST_F(read, complete_header)
{
std::string input
{
R"(ID ID1; stuff
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTT 18
//
ID ID2;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT 60
TTTTTTTTTT TTTTTTTTTT TT 82
//
ID ID3 lala;
XX
AC AB000263;
XX
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTA 7
//)"
};
options.embl_genbank_complete_header = true;
ids[0] = "ID ID1;\tstuff\n";
ids[1] = "ID ID2;\n";
ids[2] = "ID ID3 lala;\nXX\nAC AB000263;\nXX\n";
do_read_test(input);
}
TEST_F(read, multiple_lines_before_seq)
{
std::string input
{
R"(ID ID1; stuff
XX
XX
XX
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTT 18
//
ID ID2;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT 60
TTTTTTTTTT TTTTTTTTTT TT 82
//
ID ID3 lala;
SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
ACGTTTA 7
//)"
};
do_read_test(input);
}
// ----------------------------------------------------------------------------
// writing
// ----------------------------------------------------------------------------
struct write : public ::testing::Test
{
std::vector<seqan3::dna5_vector> seqs
{
"ACGT"_dna5,
"AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN"_dna5,
"GGAGTATAATATATATATATATAT"_dna5
};
std::vector<std::string> ids
{
"TEST 1",
"Test2",
"Test3"
};
std::string comp
{
R"(ID TEST 1; 4 BP.
SQ Sequence 4 BP;
ACGT 4
//
ID Test2; 91 BP.
SQ Sequence 91 BP;
AGGCTGNAGG CTGNAGGCTG NAGGCTGNAG GCTGNAGGCT GNAGGCTGNA GGCTGNAGGC 60
TGNAGGCTGN AGGCTGNAGG CTGNAGGCTG N 91
//
ID Test3; 24 BP.
SQ Sequence 24 BP;
GGAGTATAAT ATATATATAT ATAT 24
//
)"
};
seqan3::sequence_file_output_options options{};
std::ostringstream ostream;
void do_write_test()
{
seqan3::sequence_file_output fout{ostream, seqan3::format_embl{}, seqan3::fields<seqan3::field::seq,
seqan3::field::id>{}};
fout.options = options;
for (unsigned i = 0; i < 3; ++i)
EXPECT_NO_THROW((fout.emplace_back(seqs[i], ids[i])));
ostream.flush();
}
};
TEST_F(write, complete_header)
{
std::string comp
{
R"(ID TEST 1; 4 BP.
XX
SQ Sequence 4 BP;
ACGT 4
//
ID Test2; 91 BP.
XX
SQ Sequence 91 BP;
AGGCTGNAGG CTGNAGGCTG NAGGCTGNAG GCTGNAGGCT GNAGGCTGNA GGCTGNAGGC 60
TGNAGGCTGN AGGCTGNAGG CTGNAGGCTG N 91
//
ID Test3; 24 BP.
XX
SQ Sequence 24 BP;
GGAGTATAAT ATATATATAT ATAT 24
//
)"
};
options.embl_genbank_complete_header = true;
ids[0] = std::string{"ID TEST 1; 4 BP.\nXX\n"};
ids[1] = std::string{"ID Test2; 91 BP.\nXX\n"};
ids[2] = std::string{"ID Test3; 24 BP.\nXX\n"};
do_write_test();
EXPECT_EQ(ostream.str(), comp);
}
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