Пример #1
0
def poa(groups, max_sequences_per_poa=100, gpu_mem_per_batch=0.9):
    """
    Generate consensus for POA groups.

    Args:
        groups : A list of lists of sequences for which consensus is to be generated.
    """
    free, total = cuda.cuda_get_mem_info(cuda.cuda_get_device())
    gpu_mem_per_batch *= free
    batch = CudaPoaBatch(max_sequences_per_poa,
                         gpu_mem_per_batch,
                         stream=None,
                         output_type="consensus")
    results = []

    for i, group in enumerate(groups, start=1):
        group_status, seq_status = batch.add_poa_group(group)

        # Once batch is full, run POA processing
        if group_status == 1 or i == len(groups):
            batch.generate_poa()

            consensus, coverage, status = batch.get_consensus()
            results.extend(consensus)

            batch.reset()
            group_status, seq_status = batch.add_poa_group(group)

    return results
Пример #2
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def test_cudapoa_complex_batch():
    random.seed(2)
    read_len = 500
    ref = ''.join([random.choice(['A', 'C', 'G', 'T']) for _ in range(read_len)])
    num_reads = 100
    mutation_rate = 0.02
    reads = []
    for _ in range(num_reads):
        new_read = ''.join([r if random.random() > mutation_rate else random.choice(['A', 'C', 'G', 'T']) for r in ref])
        reads.append(new_read)

    device = cuda.cuda_get_device()
    free, total = cuda.cuda_get_mem_info(device)
    stream = cuda.CudaStream()
    batch = CudaPoaBatch(1000, 0.9 * free, stream=stream, device_id=device)
    (add_status, seq_status) = batch.add_poa_group(reads)
    batch.generate_poa()

    consensus, coverage, status = batch.get_consensus()

    consensus = consensus[0]
    assert(len(consensus) == len(ref))

    match_ratio = SequenceMatcher(None, ref, consensus).ratio()
    assert(match_ratio == 1.0)
Пример #3
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def test_cudapoa_simple_batch():
    free, total = cuda.cuda_get_mem_info(cuda.cuda_get_device())
    batch = CudaPoaBatch(10, 0.9 * free)
    poa_1 = ["ACTGACTG", "ACTTACTG", "ACGGACTG", "ATCGACTG"]
    poa_2 = ["ACTGAC", "ACTTAC", "ACGGAC", "ATCGAC"]
    batch.add_poa_group(poa_1)
    batch.add_poa_group(poa_2)
    batch.generate_poa()
    consensus, coverage, status = batch.get_consensus()

    assert(len(consensus) == 2)
    assert(batch.total_poas == 2)
Пример #4
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def test_cudapoa_reset_batch():
    device = cuda.cuda_get_device()
    free, total = cuda.cuda_get_mem_info(device)
    batch = CudaPoaBatch(10, 0.9 * free, device_id=device)
    poa_1 = ["ACTGACTG", "ACTTACTG", "ACGGACTG", "ATCGACTG"]
    batch.add_poa_group(poa_1)
    batch.generate_poa()
    consensus, coverage, status = batch.get_consensus()

    assert(batch.total_poas == 1)

    batch.reset()

    assert(batch.total_poas == 0)
Пример #5
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def test_cudapoa_simple_batch():
    device = cuda.cuda_get_device()
    free, total = cuda.cuda_get_mem_info(device)
    batch = CudaPoaBatch(10,
                         1024,
                         0.9 * free,
                         deivce_id=device,
                         output_mask='consensus')
    poa_1 = ["ACTGACTG", "ACTTACTG", "ACGGACTG", "ATCGACTG"]
    poa_2 = ["ACTGAC", "ACTTAC", "ACGGAC", "ATCGAC"]
    batch.add_poa_group(poa_1)
    batch.add_poa_group(poa_2)
    batch.generate_poa()
    consensus, coverage, status = batch.get_consensus()

    assert (len(consensus) == 2)
    assert (batch.total_poas == 2)
Пример #6
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def test_cudapoa_graph():
    device = cuda.cuda_get_device()
    free, total = cuda.cuda_get_mem_info(device)
    batch = CudaPoaBatch(10, 0.9 * free, device_id=device)
    poa_1 = ["ACTGACTG", "ACTTACTG", "ACTCACTG"]
    batch.add_poa_group(poa_1)
    batch.generate_poa()
    consensus, coverage, status = batch.get_consensus()

    assert (batch.total_poas == 1)

    # Expected graph
    #           - -> G -> -
    #           |         |
    # A -> C -> T -> T -> A -> C -> T -> G
    #           |         |
    #           - -> C -> -

    graphs, status = batch.get_graphs()
    assert (len(graphs) == 1)

    digraph = graphs[0]
    assert (digraph.number_of_nodes() == 10)
    assert (digraph.number_of_edges() == 11)