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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 <stdexcept>
#include <string>
#include <vector>
#include <gtest/gtest.h>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/all.hpp>
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/range/views/convert.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/std/ranges>
#include <seqan3/std/concepts>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/test/pretty_printing.hpp>
using seqan3::operator""_dna5;
using seqan3::operator""_phred42;
struct sequence_file_data : public ::testing::Test
{
std::vector<std::string> ids
{
{ "ID1" },
{ "ID2" },
{ "ID3 lala" },
};
std::vector<seqan3::dna5_vector> seqs
{
{ "ACGTTTTTTTTTTTTTTT"_dna5 },
{ "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"_dna5 },
{ "ACGTTTA"_dna5 },
};
std::vector<std::vector<seqan3::phred42>> quals
{
{ "!##$%&'()*+,-./++-"_phred42 },
{ "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE"_phred42 },
{ "!!!!!!!"_phred42 },
};
std::ostringstream ostream{};
};
template <typename format_t>
struct sequence_file_read : public sequence_file_data
{};
TYPED_TEST_SUITE_P(sequence_file_read);
// ----------------------------------------------------------------------------
// general
// ----------------------------------------------------------------------------
TYPED_TEST_P(sequence_file_read, concept_check)
{
EXPECT_TRUE((seqan3::sequence_file_input_format<TypeParam>));
}
// ----------------------------------------------------------------------------
// sequence_file_read
// ----------------------------------------------------------------------------
TYPED_TEST_P(sequence_file_read, standard)
{
std::stringstream istream{this->standard_input};
seqan3::sequence_file_input fin{istream, TypeParam{}};
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, ++it)
{
EXPECT_RANGE_EQ(seqan3::get<seqan3::field::seq>(*it), this->seqs[i]);
EXPECT_EQ(seqan3::get<seqan3::field::id>(*it), this->ids[i]);
if constexpr (std::same_as<TypeParam, seqan3::format_fastq> || std::same_as<TypeParam, seqan3::format_sam>)
{
EXPECT_RANGE_EQ(seqan3::get<seqan3::field::qual>(*it), this->quals[i]);
}
}
}
TYPED_TEST_P(sequence_file_read, only_seq)
{
std::stringstream istream{this->standard_input};
seqan3::sequence_file_input fin{istream, TypeParam{}, seqan3::fields<seqan3::field::seq>{}};
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, ++it)
EXPECT_EQ(std::get<0>(*it), this->seqs[i]);
}
TYPED_TEST_P(sequence_file_read, only_id)
{
std::stringstream istream{this->standard_input};
seqan3::sequence_file_input fin{istream, TypeParam{}, seqan3::fields<seqan3::field::id>{}};
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, ++it)
EXPECT_EQ(std::get<0>(*it), this->ids[i]);
}
TYPED_TEST_P(sequence_file_read, seq_qual)
{
std::stringstream istream{this->standard_input};
seqan3::sequence_file_input fin{istream, TypeParam{}, seqan3::fields<seqan3::field::id, seqan3::field::seq_qual>{}};
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, ++it)
{
EXPECT_RANGE_EQ(seqan3::get<seqan3::field::id>(*it), this->ids[i]);
EXPECT_RANGE_EQ(seqan3::get<seqan3::field::seq_qual>(*it) | seqan3::views::convert<seqan3::dna5>,
this->seqs[i]);
}
}
TYPED_TEST_P(sequence_file_read, options_truncate_ids)
{
std::stringstream istream{this->standard_input};
seqan3::sequence_file_input fin{istream, TypeParam{}, seqan3::fields<seqan3::field::id>{}};
fin.options.truncate_ids = true;
this->ids[2] = "ID3"; // "lala" is stripped
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, ++it)
EXPECT_EQ(std::get<0>(*it), this->ids[i]);
}
TYPED_TEST_P(sequence_file_read, illegal_alphabet_character)
{
std::stringstream istream{this->illegal_alphabet_character_input};
seqan3::sequence_file_input fin{istream, TypeParam{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}
TYPED_TEST_P(sequence_file_read, no_or_ill_formatted_id)
{
std::stringstream istream{this->no_or_ill_formatted_id_input};
seqan3::sequence_file_input fin{istream, TypeParam{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}
// ----------------------------------------------------------------------------
// sequence_file_write
// ----------------------------------------------------------------------------
template <typename format_type>
struct sequence_file_write : public sequence_file_read<format_type>
{};
TYPED_TEST_SUITE_P(sequence_file_write);
TYPED_TEST_P(sequence_file_write, concept_check)
{
EXPECT_TRUE((seqan3::sequence_file_output_format<TypeParam>));
}
TYPED_TEST_P(sequence_file_write, standard)
{
seqan3::sequence_file_output fout{this->ostream, TypeParam{}};
for (unsigned i = 0; i < 3; ++i)
EXPECT_NO_THROW((fout.emplace_back(this->seqs[i], this->ids[i], this->quals[i])));
this->ostream.flush();
EXPECT_EQ(this->ostream.str(), this->standard_output);
}
TYPED_TEST_P(sequence_file_write, seq_qual)
{
auto convert_to_qualified = std::views::transform([] (auto const in)
{
return seqan3::qualified<seqan3::dna5, seqan3::phred42>{std::get<0>(in), std::get<1>(in)};
});
seqan3::sequence_file_output fout{this->ostream, TypeParam{}, seqan3::fields<seqan3::field::id,
seqan3::field::seq_qual>{}};
for (unsigned i = 0; i < 3; ++i)
{
EXPECT_NO_THROW((fout.emplace_back(this->ids[i],
seqan3::views::zip(this->seqs[i], this->quals[i]) | convert_to_qualified)));
}
this->ostream.flush();
EXPECT_EQ(this->ostream.str(), this->standard_output);
}
TYPED_TEST_P(sequence_file_write, arg_handling_id_missing)
{
if constexpr (!std::same_as<TypeParam, seqan3::format_sam>)
{
seqan3::sequence_file_output fout{this->ostream, TypeParam{}, seqan3::fields<seqan3::field::seq>{}};
EXPECT_THROW((fout.emplace_back(this->seqs[0])), std::logic_error);
}
}
TYPED_TEST_P(sequence_file_write, arg_handling_id_empty)
{
if constexpr (!std::same_as<TypeParam, seqan3::format_sam>)
{
seqan3::sequence_file_output fout{this->ostream, TypeParam{}, seqan3::fields<seqan3::field::seq,
seqan3::field::id>{}};
EXPECT_THROW((fout.emplace_back(this->seqs[0], std::string_view{""}, std::ignore)), std::runtime_error);
}
}
TYPED_TEST_P(sequence_file_write, arg_handling_seq_missing)
{
if constexpr (!std::same_as<TypeParam, seqan3::format_sam>)
{
seqan3::sequence_file_output fout{this->ostream, TypeParam{}, seqan3::fields<seqan3::field::id>{}};
EXPECT_THROW((fout.emplace_back(this->ids[0])), std::logic_error);
}
}
TYPED_TEST_P(sequence_file_write, arg_handling_seq_empty)
{
if constexpr (!std::same_as<TypeParam, seqan3::format_sam>)
{
seqan3::sequence_file_output fout{this->ostream, TypeParam{}, seqan3::fields<seqan3::field::seq,
seqan3::field::id>{}};
EXPECT_THROW((fout.emplace_back(std::string_view{""}, this->ids[0], std::ignore)), std::runtime_error);
}
}
REGISTER_TYPED_TEST_SUITE_P(sequence_file_read,
concept_check,
standard,
only_seq,
only_id,
seq_qual,
illegal_alphabet_character,
options_truncate_ids,
no_or_ill_formatted_id);
REGISTER_TYPED_TEST_SUITE_P(sequence_file_write,
concept_check,
standard,
seq_qual,
arg_handling_id_missing,
arg_handling_id_empty,
arg_handling_seq_missing,
arg_handling_seq_empty);
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