def test_graph_parser_streaming(benchmark, graph_size, func_type):
graph = GRAPHS[graph_size]
func = FUNCS[func_type]
buffer = io.BytesIO(open(graph, 'rb').read())
header = Header.from_stream(buffer)
buffer = io.BytesIO(buffer.read())
benchmark(func, buffer, header)
def test_parses_a_graph_header(self, tmpdir):
# given
sample_name = 'sample_0'
dna_sequence = 'ACGTT'
kmer_size = 3
mc_builder = (builder.Mccortex().with_dna_sequence(
dna_sequence, name=sample_name).with_kmer_size(kmer_size))
output_graph = mc_builder.build(tmpdir)
expected_header_attributes = {
'version': 6,
'kmer_size': kmer_size,
'record_size': 13,
'kmer_container_size': 1,
'num_colors': 1,
'mean_read_lengths': (len(dna_sequence), ),
'total_sequences': (len(dna_sequence), ),
'sample_names': (sample_name.encode(), )
}
# when
header = Header.from_stream(open(output_graph, 'rb'))
# then
for key, value in expected_header_attributes.items():
assert getattr(header, key) == value
def test_index(self, data, kmer_size, n_kmers):
# given
assume(kmer_size % 2 == 1)
num_colors = 1
graph_builder = (builder.Graph().with_kmer_size(
kmer_size).with_num_colors(num_colors))
expected_kmers = []
seen_kmers = set()
for _ in range(n_kmers):
kmer = data.draw(kmer_records(kmer_size, num_colors))
while kmer.kmer in seen_kmers:
kmer = data.draw(kmer_records(kmer_size, num_colors))
seen_kmers.add(kmer.kmer)
graph_builder.with_kmer_record(kmer)
expected_kmers.append(kmer)
expected_kmers = sorted(expected_kmers)
graph_stream = graph_builder.build()
header_stream = graph_builder.header.build()
header = Header.from_stream(header_stream)
# when
sequence = KmerUintSequence(graph_handle=graph_stream,
body_start=len(header_stream.getvalue()),
header=header,
n_records=len(expected_kmers))
# then
for idx, expected_kmer in enumerate(expected_kmers):
# then
assert idx == sequence.index_kmer_string(expected_kmer.kmer)
def header(self):
color_info_blocks = [
ColorInformationBlock() for _ in range(self.num_colors)
]
return Header(kmer_size=self.kmer_size,
kmer_container_size=self.kmer_container_size,
num_colors=self.num_colors,
sample_names=self.sample_names,
color_info_blocks=color_info_blocks)
def test_cython_speed():
graph = 'fixtures/yeast/NC_001133.9.16kbp.ctx'
buffer = io.BytesIO(open(graph, 'rb').read())
header = Header.from_stream(buffer)
buffer = io.BytesIO(buffer.read())
cProfile.runctx("stream_kmers_and_coverage_and_edges(buffer, header)", globals(), locals(),
"Profile.prof")
s = pstats.Stats("Profile.prof")
raise Exception(s.strip_dirs().sort_stats("time").print_stats())
def test_does_not_raise(self):
# given
graph_header_fixture = os.path.join(os.path.dirname(__file__),
'many_colors_header_only.ctx')
# when
with open(graph_header_fixture, 'rb') as header_handle:
header = Header.from_stream(header_handle)
# then
assert header.version == 6
assert header.kmer_size == 47
assert header.kmer_container_size == 2
assert header.num_colors == 25
def kmer_generator_from_stream(stream):
header = Header.from_stream(stream)
return kmer_generator_from_stream_and_header(stream, header)
def load_cortex_graph(stream):
header = Header.from_stream(stream)
kmer_generator = kmer_generator_from_stream_and_header(stream, header)
return build_cortex_graph_from_header(header,
kmer_generator=kmer_generator)