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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
// -----------------------------------------------------------------------------------------------------
#include <sstream>
#include <string>
#include <gtest/gtest.h>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/test/pretty_printing.hpp>
#include "sequence_file_format_test_template.hpp"
template <>
struct sequence_file_read<seqan3::format_genbank> : public sequence_file_data
{
std::string standard_input
{
R"(LOCUS ID1
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID1
ACCESSION U49845
VERSION U49845.1 GI:1293613
KEYWORDS .
SOURCE Saccharomyces cerevisiae (baker's yeast)
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
Saccharomycetales; Saccharomycetaceae; Saccharomyces.
REFERENCE 1 (bases 1 to 5028)
FEATURES Location/Qualifiers
source 1..5028
ORIGIN
1 ACGTTTTTTT TTTTTTTT
//
LOCUS ID2
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID2
ORIGIN
1 ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT
61 TTTTTTTTTT TTTTTTTTTT TT
//
LOCUS ID3 lala
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID3
ORIGIN
1 ACGTTTA
//
)"
};
std::string illegal_alphabet_character_input
{
R"(LOCUS ID1
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID1
ORIGIN
1 ACGTTTT?TT TTTTTTTT
//
)"
};
std::string standard_output
{
R"(LOCUS ID1 18 bp
ORIGIN
1 ACGTTTTTTT TTTTTTTT
//
LOCUS ID2 82 bp
ORIGIN
1 ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT
61 TTTTTTTTTT TTTTTTTTTT TT
//
LOCUS ID3 lala 7 bp
ORIGIN
1 ACGTTTA
//
)"
};
std::string no_or_ill_formatted_id_input
{
R"(LOCOS ID1 stuff
ORIGIN
1 ACGTTTTTTT TTTTTTTT
//
)"
};
};
// ---------------------------------------------------------------------------------------------------------------------
// parametrized tests
// ---------------------------------------------------------------------------------------------------------------------
INSTANTIATE_TYPED_TEST_SUITE_P(genbank, sequence_file_read, seqan3::format_genbank, );
INSTANTIATE_TYPED_TEST_SUITE_P(genbank, sequence_file_write, seqan3::format_genbank, );
// ----------------------------------------------------------------------------
// reading
// ----------------------------------------------------------------------------
struct read : public sequence_file_read<seqan3::format_genbank>
{
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_genbank{}};
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)
{
options.embl_genbank_complete_header = true;
ids[0] = R"(LOCUS ID1
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID1
ACCESSION U49845
VERSION U49845.1 GI:1293613
KEYWORDS .
SOURCE Saccharomyces cerevisiae (baker's yeast)
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
Saccharomycetales; Saccharomycetaceae; Saccharomyces.
REFERENCE 1 (bases 1 to 5028)
FEATURES Location/Qualifiers
source 1..5028
)";
ids[1] = R"(LOCUS ID2
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID2
)";
ids[2] = R"(LOCUS ID3 lala
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID3
)";
do_read_test(standard_input);
}
// ----------------------------------------------------------------------------
// writing
// ----------------------------------------------------------------------------
struct write : public sequence_file_data
{
seqan3::sequence_file_output_options options{};
std::ostringstream ostream;
void do_write_test()
{
seqan3::sequence_file_output fout{ostream, seqan3::format_genbank{}, 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"(LOCUS ID1 18 bp
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID1
VERSION ID1
KEYWORDS .
SOURCE .
ORGANISM .
ORIGIN
1 ACGTTTTTTT TTTTTTTT
//
LOCUS ID2 82 bp
DEFINITION ID2
ACCESSION ID2
VERSION ID2
KEYWORDS .
SOURCE .
ORGANISM .
ORIGIN
1 ACGTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT
61 TTTTTTTTTT TTTTTTTTTT TT
//
LOCUS ID3 7 bp
DEFINITION ID3
ACCESSION ID3
VERSION ID3
KEYWORDS .
SOURCE .
ORGANISM .
ORIGIN
1 ACGTTTA
//
)"
};
options.embl_genbank_complete_header = true;
ids[0] = R"(LOCUS ID1 18 bp
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds.
ACCESSION ID1
VERSION ID1
KEYWORDS .
SOURCE .
ORGANISM .
)";
ids[1] = R"(LOCUS ID2 82 bp
DEFINITION ID2
ACCESSION ID2
VERSION ID2
KEYWORDS .
SOURCE .
ORGANISM .
)";
ids[2] = R"(LOCUS ID3 7 bp
DEFINITION ID3
ACCESSION ID3
VERSION ID3
KEYWORDS .
SOURCE .
ORGANISM .
)";
do_write_test();
EXPECT_EQ(ostream.str(), comp);
}
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