Python protein_to_transcript Examples

Example #1

File: test_ncbi.py Project: zyj0808/mutalyzer

def test_protein_to_transcript_cache(accession, version, match_version,
                                     expected_forward, expected_reverse):
    """
    Get transcript for protein and check the resulting cache state.
    """
    try:
        ncbi.protein_to_transcript(accession, version, match_version)
    except ncbi.NoLinkError:
        pass

    forward = [(key.split(':')[-1], redis.get(key) or None)
               for key in redis.keys('ncbi:transcript-to-protein:*')]
    assert sorted(forward) == sorted(expected_forward)

    reverse = [(redis.get(key) or None, key.split(':')[-1])
               for key in redis.keys('ncbi:protein-to-transcript:*')]
    assert sorted(reverse) == sorted(expected_reverse)

Example #2

File: test_ncbi.py Project: chenyu600/mutalyzer

def test_protein_to_transcript_cache(accession, version, match_version,
                                     expected_forward, expected_reverse):
    """
    Get transcript for protein and check the resulting cache state.
    """
    try:
        ncbi.protein_to_transcript(accession, version, match_version)
    except ncbi.NoLinkError:
        pass

    forward = [(key.split(':')[-1], redis.get(key) or None)
               for key in redis.keys('ncbi:transcript-to-protein:*')]
    assert sorted(forward) == sorted(expected_forward)

    reverse = [(redis.get(key) or None, key.split(':')[-1])
               for key in redis.keys('ncbi:protein-to-transcript:*')]
    assert sorted(reverse) == sorted(expected_reverse)

Example #3

File: test_ncbi.py Project: zyj0808/mutalyzer

def test_protein_to_transcript(accession, version, match_version, expected):
    """
    Get transcript for protein.

    Both the Entrez API and our cache are fixed with a set of
    transcript-protein links. This test is parametrized with a list of
    arguments for the :func:`ncbi.transcript_to_protein` function and the
    corresponding expected result.

    Fixtures and parameters of this test mirror those of the
    `test_transcript_to_protein` test.
    """
    if expected is None:
        with pytest.raises(ncbi.NoLinkError):
            ncbi.protein_to_transcript(accession, version, match_version)
    else:
        assert ncbi.protein_to_transcript(accession, version,
                                          match_version) == expected

Example #4

File: test_ncbi.py Project: chenyu600/mutalyzer

def test_protein_to_transcript(accession, version, match_version, expected):
    """
    Get transcript for protein.

    Both the Entrez API and our cache are fixed with a set of
    transcript-protein links. This test is parametrized with a list of
    arguments for the :func:`ncbi.transcript_to_protein` function and the
    corresponding expected result.

    Fixtures and parameters of this test mirror those of the
    `test_transcript_to_protein` test.
    """
    if expected is None:
        with pytest.raises(ncbi.NoLinkError):
            ncbi.protein_to_transcript(accession, version, match_version)
    else:
        assert ncbi.protein_to_transcript(
            accession, version, match_version) == expected