test_assemble.py 文件源码

def test_graph_init():
    """Test graph initialization."""
    instream = kevlar.open(data_file('var1.reads.augfastq'), 'r')
    graph = kevlar.ReadGraph()
    graph.load(kevlar.parse_augmented_fastx(instream))
    graph.populate_edges(strict=True)

    # 10 reads in the file, but read16f has no valid connections due to error
    assert len(graph.nodes()) == 10

    # The given read shares its interesting k-mer and has compatible overlaps
    # with 6 other reads (read13f and read15f have errors).
    r23name = 'read23f start=67,mutations=0'
    assert len(graph[r23name]) == 6

    # Test the values of one of the edges.
    r35name = 'read35f start=25,mutations=0'
    assert graph[r23name][r35name]['offset'] == 42
    assert graph[r23name][r35name]['overlap'] == 58

    # Should all be a single CC
    assert len(list(connected_components(graph))) == 2
    assert len([p for p in graph.partitions()]) == 1

    r8name = 'read8f start=8,mutations=0'
    r37name = 'read37f start=9,mutations=0'
    assert graph[r37name][r8name]['offset'] == 1
    assert graph[r37name][r8name]['overlap'] == 99
    pair = OverlappingReadPair(
        tail=graph.get_record(r8name), head=graph.get_record(r37name),
        offset=1, overlap=99, sameorient=True, swapped=False
    )
    assert merge_pair(pair) == ('CACTGTCCTTACAGGTGGATAGTCGCTTTGTAATAAAAGAGTTAC'
                                'ACCCCGGTTTTTAGAAGTCTCGACTTTAAGGAAGTGGGCCTACGG'
                                'CGGAAGCCGTC')