FastaIO.cc

#include <Sequence/Fasta.hpp>
#include <fstream>
#include <iostream>
#include <boost/test/unit_test.hpp>
#include <unistd.h>
#include <iterator>

struct fasta_io_fixture
{
    std::string name, seq, seq_left, seq_right;
    fasta_io_fixture()
        : name{ "seqname is a seq" }, seq{ "AGCGTAGACAGTAGAGTGAT" },
          seq_left{ "AGCGTAGAC" }, seq_right{ "AGTAGAGTGAT" }
    {
    }
};

BOOST_FIXTURE_TEST_SUITE(FastaIOTest,fasta_io_fixture)

BOOST_AUTO_TEST_CASE(ostream_test)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    Sequence::Fasta f(name, seq), f2;
    std::ofstream o(filename);
    o << f << std::endl;
    o.close();
    std::ifstream in(filename);
    in >> f2 >> std::ws;
    BOOST_REQUIRE_EQUAL(f, f2);
    unlink(filename);
}

BOOST_AUTO_TEST_CASE(ostream_test_3recs)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    Sequence::Fasta f(name, seq), f2;
    std::ofstream o(filename);
    o << f << '\n' << f << '\n' << f << '\n';
    o.close();
    std::ifstream in(filename);
    unsigned count = 0;
    while (!in.eof())
        {
            in >> f2 >> std::ws;
            BOOST_REQUIRE_EQUAL(f.name, f2.name);
            BOOST_REQUIRE_EQUAL(f.seq, f2.seq);
            ++count;
        }
    BOOST_REQUIRE_EQUAL(count, 3);
    //in >> f2 >> std::ws;

    unlink(filename);
}

//No newline @ end of data
BOOST_AUTO_TEST_CASE(ostream_test_no_newline_end_of_file)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    Sequence::Fasta f(name, seq), f2;
    std::ofstream o(filename);
    o << f << '\n' << f << '\n' << f;
    o.close();
    std::ifstream in(filename);
    unsigned count = 0;
    while (!in.eof())
        {
            in >> f2 >> std::ws;
            BOOST_REQUIRE_EQUAL(f.name, f2.name);
            BOOST_REQUIRE_EQUAL(f.seq, f2.seq);
            ++count;
        }
    BOOST_REQUIRE_EQUAL(count, 3);
    unlink(filename);
}

BOOST_AUTO_TEST_CASE(ostream_test_newline_within_seq)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    Sequence::Fasta f(name, seq), f2;
    std::ofstream o(filename);
    for (unsigned i = 0; i < 3; ++i)
        {
            o << '>' << name << '\n' << seq_left << '\n' << seq_right << '\n';
        }
    o.close();
    std::ifstream in(filename);
    unsigned count = 0;
    while (!in.eof())
        {
            in >> f2 >> std::ws;
            BOOST_REQUIRE_EQUAL(f.name, f2.name);
            BOOST_REQUIRE_EQUAL(f.seq, f2.seq);
            ++count;
        }
    BOOST_REQUIRE_EQUAL(count, 3);
    unlink(filename);
}

BOOST_AUTO_TEST_CASE(ostream_test_really_bad_input)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    Sequence::Fasta f(name, seq), f2;
    std::ofstream o(filename);
    for (unsigned i = 0; i < 3; ++i)
        {
            o << '>' << name << '\n'
              << seq_left << "\n\n\n\n\n" //Bad bad bad
              << seq_right << '\n';
        }
    o.close();
    std::ifstream in(filename);
    unsigned count = 0;
    while (!in.eof())
        {
            in >> f2 >> std::ws;
            BOOST_REQUIRE_EQUAL(f.name, f2.name);
            BOOST_REQUIRE_EQUAL(f.seq, f2.seq);
            ++count;
        }
    BOOST_REQUIRE_EQUAL(count, 3);
    unlink(filename);
}

BOOST_AUTO_TEST_CASE(ostream_test_really_bad_input_istream_iterator)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    Sequence::Fasta f(name, seq), f2;
    std::ofstream o(filename);
    for (unsigned i = 0; i < 3; ++i)
        {
            o << '>' << name << '\n'
              << seq_left << "\n\n\n\n\n" //Bad bad bad
              << seq_right << '\n';
        }
    o.close();
    std::ifstream in(filename);
    unsigned count = 0;
    std::istream_iterator<Sequence::Fasta> i(in);
    for (; i != std::istream_iterator<Sequence::Fasta>(); ++i)
        {
            ++count;
        }
    BOOST_REQUIRE_EQUAL(count, 3);
    unlink(filename);
}

BOOST_AUTO_TEST_CASE(exception_test)
{
    const char* filename = "fasta_ostream_test_out.fasta";
    std::ofstream out(filename);
    //Write a badly-formatted FASTA record (we forgot the >)
    out << name << '\n' << seq;
    out.close();

    std::ifstream in(filename);
    Sequence::Fasta f;
    BOOST_CHECK_THROW(in >> f >> std::ws, std::runtime_error);
    unlink(filename);
}

BOOST_AUTO_TEST_SUITE_END()
//EOF