def _run(self):
mccortex_graphs = []
self.mccortex_builders.append(self.mccortex_builder)
for idx, mc_builder in enumerate(self.mccortex_builders):
mc_builder.with_kmer_size(self.kmer_size)
builder_dir = self.tmpdir / 'mc_graph_{}'.format(idx)
builder_dir.mkdir()
mc_graph, _ = mc_builder.build(builder_dir)
mccortex_graphs.append(mc_graph)
contig_fasta = self._write_contig_fasta()
self.traversal = self.tmpdir / 'traversal.ctx'
if self.spawn_process is None:
ctp_runner = runner.Cortexpy(SPAWN_PROCESS)
else:
ctp_runner = runner.Cortexpy(self.spawn_process)
return ctp_runner.subgraph(
graphs=mccortex_graphs,
out=self.traversal,
contig=contig_fasta,
contig_fasta=True,
verbose=self.verbose,
silent=self.silent,
colors=self.colors,
logging_interval=self.logging_interval_seconds)
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 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 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):
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_prints_single_kmer(self, tmpdir):
# given
kmer_size = 3
output_graph = (builder.Mccortex().with_dna_sequence(
'ACCAA').with_kmer_size(kmer_size).build(tmpdir))
expected_kmer = 'CAA: CAA 1 1 .c...... ........'
# when
stdout = runner.Cortexpy().view_contig(graph=output_graph,
contig='CAA').stdout
# then
assert [expected_kmer
] == CortexpyPrintOutputParser(stdout).get_kmer_strings()
def test_with_empty_input_outputs_empty_fasta(self, tmpdir):
# given
input_graph = str(tmpdir / 'input.gfa')
output_graph = tmpdir / 'output.fast'
with open(input_graph, 'w') as fh:
fh.write(GfaBuilder().build())
# when
runner.Cortexpy().traverse(input_graph,
out=output_graph,
input_gfa=True)
# then
expect = Fasta(output_graph.read())
expect.has_no_records()
def test_prints_one_missing_kmer(self, tmpdir):
# given
kmer_size = 3
record = 'GGG'
output_graph = (builder.Mccortex().with_dna_sequence(
'AAAA').with_kmer_size(kmer_size).build(tmpdir))
expected_kmer = 'CCC: GGG 0 1 ........ ........'
# when
stdout = runner.Cortexpy().view_contig(graph=output_graph,
contig=record).stdout
# then
assert [expected_kmer
] == CortexpyPrintOutputParser(stdout).get_kmer_strings()
def test_does_not_raise_without_max_nodes(self, tmpdir):
# given
query = 'CAACC'
records = [query]
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(True).subgraph(graphs=[output_graph],
contig=query,
out=tmpdir / 'discarded.pickle',
)
# then
assert 0 == completed_process.returncode
def test_raises_on_max_nodes_exceeded(self, tmpdir):
# given
query = 'CAA'
records = ['CAACC']
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=True).subgraph(graphs=[output_graph],
contig=query,
max_nodes=1)
# then
assert 0 != completed_process.returncode
assert 'Max nodes (1) exceeded: 3 nodes found' in completed_process.stderr
def test_prints_three_kmers_including_one_revcomp(self, tmpdir):
# given
record = 'ACCTT'
kmer_size = 3
output_graph = (builder.Mccortex().with_dna_sequence(
record).with_kmer_size(kmer_size).build(tmpdir))
expected_kmers = [
'AAG 1 ......G.',
'ACC 1 .......T',
'AGG 1 a......T',
]
# when
stdout = runner.Cortexpy().view_graph(output_graph).stdout
# then
assert expected_kmers == CortexpyPrintOutputParser(
stdout).get_kmer_strings()
def run(self):
mccortex_graph = self.mccortex_builder.build(self.tmpdir)
contig_fasta = self.tmpdir / 'initial_contigs.fa'
with open(str(contig_fasta), 'w') as fh:
SeqIO.write(self.records, fh, 'fasta')
ctp_runner = runner.Cortexpy(SPAWN_PROCESS)
pruned_graph = Path(str(mccortex_graph)).with_suffix('.pruned.ctx')
completed_process = ctp_runner.prune(graph=mccortex_graph,
out=pruned_graph,
remove_tips=self.min_tip_length,
verbose=True)
assert completed_process.returncode == 0, completed_process
print(completed_process.stdout)
print(completed_process.stderr, file=sys.stderr)
return expectation.graph.KmerGraphExpectation(
load_cortex_graph(pruned_graph))
def test_prints_three_kmers(self, tmpdir):
# given
record = 'ACCAA'
kmer_size = 3
output_graph = (builder.Mccortex().with_dna_sequence(
record).with_kmer_size(kmer_size).build(tmpdir))
expected_kmers = [
'ACC: ACC 1 1 ....A... ....A...',
'CCA: CCA 1 1 a...A... a...A...',
'CAA: CAA 1 1 .c...... .c......',
]
# when
stdout = runner.Cortexpy().view_contig(graph=output_graph,
contig=record).stdout
# then
assert expected_kmers == CortexpyPrintOutputParser(
stdout).get_kmer_strings()
def test_prints_one_missing_and_one_revcomp_kmer(self, tmpdir):
# given
dna_sequence = 'ACCTT'
search_record = 'ACTT'
kmer_size = 3
output_graph = (builder.Mccortex().with_dna_sequence(
dna_sequence).with_kmer_size(kmer_size).build(tmpdir))
expected_kmers = [
'ACT: ACT 0 1 ........ .......T',
'AAG: CTT 1 1 .C...... A.......',
]
# when
stdout = runner.Cortexpy().view_contig(graph=output_graph,
contig=search_record).stdout
expect = ViewExpectation(stdout)
# then
(expect.has_kmer(expected_kmers[0]).has_kmer(
expected_kmers[1]).has_n_kmers(2))
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)
