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
def test_cudapoa_reset_batch():
free, total = cuda.cuda_get_mem_info(cuda.cuda_get_device())
batch = CudaPoaBatch(10, 0.9 * free)
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)