def test_outputs_contigs_for_bubble(self, tmpdir):
# given
records = [
'AAACCC',
'AAAGCCC',
]
kmer_size = 3
maker = builder.Mccortex().with_kmer_size(kmer_size)
for rec in records:
maker.with_dna_sequence(rec)
output_graph = maker.build(tmpdir)
# when
completed_process = runner.Cortexpy(SPAWN_PROCESS) \
.traverse(graph=output_graph, contig='AAA')
stdout = completed_process.stdout
# then
assert completed_process.returncode == 0, completed_process
expect = expectation.Fasta(stdout)
for record in records:
expect.has_record(record)
expect.has_n_records(2)
def test_dal19_data(self, tmpdir):
# given
records = [
'CCCCGAGGGAAGCTCTATGAATTCGCCAATCCCAGTATGCAAAAAATGTTGGAGAGGTATCAAAAGTATTCACAAGAAAGT',
'GTATGCAAAAAATGTTGGAGAGGTATCAAAAGTATTCACAAGAAAGTGACATA',
'TAAAAAATGTTGGAGAGGTATCAAAAGTATTCACAAGAAAGTGACATAGATAACACTACCAAAGAGCAAGACTATCAG'
]
expected_records = [records[0] + records[1][47:] + records[2][48:], records[2]]
kmer_size = 47
maker = builder.Mccortex().with_kmer_size(kmer_size)
for rec in records:
maker.with_dna_sequence(rec)
output_graph = maker.build(tmpdir)
# when
completed_process = runner.Cortexpy(SPAWN_PROCESS) \
.traverse(to_json=False,
graph=output_graph,
contig='CAAAAAATGTTGGAGAGGTATCAAAAGTATTCACAAGAAAGTGACAT')
stdout = completed_process.stdout
# then
assert completed_process.returncode == 0, completed_process
expect = expectation.Fasta(stdout)
for record in expected_records:
expect.has_record(record)
expect.has_n_records(2)
def test_outputs_multiple_combinations(self, tmpdir):
# given
records = [
'CAACC',
'AAACA',
'AAACT',
]
n_paths = 6
kmer_size = 3
maker = builder.Mccortex().with_kmer_size(kmer_size)
for rec in records:
maker.with_dna_sequence(rec)
output_graph = maker.build(tmpdir)
# when
completed_process = (
runner.Cortexpy(SPAWN_PROCESS).traverse(to_json=False,
graph=output_graph,
contig='AAA')
)
stdout = completed_process.stdout
# then
assert completed_process.returncode == 0, completed_process
expect = expectation.Fasta(stdout)
ids = ['g0_p{}'.format(i) for i in range(n_paths)]
for record in records:
expect.has_record(record).has_id_in(*ids)
expect.has_record('CAACT').has_id_in(*ids)
expect.has_record('CAACA').has_id_in(*ids)
expect.has_record('AAACC').has_id_in(*ids)
expect.has_n_records(6)
def run(self):
self.traverse_driver.run()
if self.subgraphs:
assert self.to_json
out_prefix = Path(str(self.tmpdir)) / 'subgraphs'
else:
out_prefix = None
links = self.link_builder.build(self.tmpdir,
self.traverse_driver.traversal)
ret = runner.Cortexpy(SPAWN_PROCESS).traverse(
self.traverse_driver.traversal,
to_json=self.to_json,
contig=self.seed_strings,
graph_index=self.graph_index,
extra_start_kmer=self.extra_start_kmer,
links_file=links)
print(ret.stdout)
print(ret.stderr, file=sys.stderr)
assert ret.returncode == 0, ret
if self.to_json:
if self.subgraphs:
return expectation.JsonGraphs(
list(out_prefix.parent.glob(out_prefix.name + '*')))
else:
return expectation.JsonGraph(json.loads(ret.stdout))
return expectation.Fasta(ret.stdout)
def run(self):
inital_seq_fasta = self.tmpdir / 'initial_seqs.fasta'
initial_seqs = [
SeqRecord(Seq(rec), id=str(idx))
for idx, rec in enumerate(self.initial_seqs)
]
SeqIO.write(initial_seqs, str(inital_seq_fasta), "fasta")
output_graph = self.mccortex_builder.build(self.tmpdir)
output = self.tmpdir / 'output.fa'
completed_process = runner.Cortexpy(SPAWN_PROCESS).assemble(
graph=output_graph, initial_seqs=inital_seq_fasta, out=output)
assert completed_process.returncode == 0, completed_process
return expectation.Fasta(open(output, 'r').read())
def test_outputs_fasta_of_kmers(self, tmpdir):
# given
record = 'ATTCC'
kmer_size = 3
output_graph = builder.Mccortex() \
.with_dna_sequence(record) \
.with_kmer_size(kmer_size) \
.build(tmpdir)
# when
completed_process = runner.Cortexpy(SPAWN_PROCESS) \
.view_graph(kmers=True, graph=output_graph)
stdout = completed_process.stdout
# then
assert completed_process.returncode == 0, completed_process
expect = expectation.Fasta(stdout)
expect.has_record('AAT')
expect.has_record('GAA')
expect.has_record('GGA')
expect.has_n_records(3)
def test_raises_on_max_path_1_exceeded(self, tmpdir, max_paths):
# given
MAX_PATH_EXIT_CODE = 64
records = ['CAACC', 'CAACT']
kmer_size = 3
maker = builder.Mccortex().with_kmer_size(kmer_size)
for rec in records:
maker.with_dna_sequence(rec)
# when
completed_process = runner.Cortexpy(spawn_process=True).traverse(
graph=maker.build(tmpdir),
max_paths=max_paths)
# then
if max_paths == 1:
assert MAX_PATH_EXIT_CODE == completed_process.returncode
assert f'Max paths ({max_paths}) exceeded' in completed_process.stderr
else:
assert 0 == completed_process.returncode
expect = expectation.Fasta(completed_process.stdout)
expect.has_record('CAACC')
expect.has_record('CAACT')
expect.has_n_records(2)