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 test_with_bubble_and_two_colors_returns_all_kmers(
self, tmpdir, ra_constructor):
# given
kmer_size = 3
output_graph = (builder.Mccortex(kmer_size).with_dna_sequence(
'AAACAAG').with_dna_sequence('AAATAAG').with_dna_sequence(
'AAATAAG', name='sample_1').build(tmpdir))
traverser = Engine(ra_constructor(open(output_graph, 'rb')),
traversal_colors=(0, ),
orientation=EngineTraversalOrientation.both)
# when
expect = KmerGraphExpectation(traverser.traverse_from('ACA').graph,
sort_edges=True)
# then
expect.has_node('AAA').has_coverages(2, 1)
expect.has_node('AAC').has_coverages(1, 0)
expect.has_node('ACA').has_coverages(1, 0)
expect.has_node('CAA').has_coverages(1, 0)
expect.has_node('AAG').has_coverages(2, 1)
expect.has_node('AAT').has_coverages(1, 1)
expect.has_node('ATA').has_coverages(1, 1)
expect.has_node('TAA').has_coverages(1, 1)
expect.has_edges('AAA AAC 0', 'AAC ACA 0', 'ACA CAA 0', 'CAA AAG 0',
'AAA AAT 0', 'AAT ATA 0', 'ATA TAA 0', 'TAA AAG 0',
'AAA AAT 1', 'AAT ATA 1', 'ATA TAA 1', 'AAG TAA 1')
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_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_three_linked_kmers_and_two_colors_returns_three_kmers(
self, tmpdir):
# given
kmer_size = 3
output_graph = (builder.Mccortex(kmer_size).with_dna_sequence(
'AAAC').with_dna_sequence('AAAT').build(tmpdir))
retriever = ContigRetriever(open(output_graph, 'rb'))
# when
kmer_graph = retriever.get_kmer_graph('GTTT')
# then
assert set(kmer_graph.nodes) == {'TTT', 'GTT', 'ATT'}
assert set(kmer_graph.edges) == {('GTT', 'TTT', 0), ('GTT', 'TTT', 1),
('ATT', 'TTT', 0)}
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_with_two_subgraphs_returns_all_kmers(self, tmpdir,
ra_constructor):
# given
kmer_size = 3
output_graph = (builder.Mccortex(kmer_size).with_dna_sequence(
'AAAT').with_dna_sequence('GGGC').build(tmpdir))
traverser = Engine(ra_constructor(open(output_graph, 'rb')),
traversal_colors=(0, ),
orientation=EngineTraversalOrientation.both)
# when
expect = KmerGraphExpectation(
traverser.traverse_from_each_kmer_in_iterable(['AAA',
'GGG']).graph)
# then
expect.has_edges('AAA AAT 0', 'CCC GCC 0')
def test_outputs_json(self, tmpdir):
# given
record = 'ACCTT'
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_contig(to_json=True, graph=output_graph, contig=record)
stdout = completed_process.stdout
# then
assert completed_process.returncode == 0, completed_process
expect = JsonGraph(json.loads(stdout))
expect.is_directed()
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_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_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 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_collapse_kmer_unitigs_option_with_missing_kmers(self, tmpdir):
# given
record1 = 'AAACCCGAA'
record2 = 'ACCG'
query_record = record1 + 'G'
kmer_size = 3
output_graph = builder.Mccortex() \
.with_dna_sequence(record1) \
.with_dna_sequence(record2) \
.with_kmer_size(kmer_size) \
.build(tmpdir)
runner.Mccortex(kmer_size).view(output_graph)
# when
completed_process = runner \
.Cortexpy(SPAWN_PROCESS) \
.view_contig(contig=query_record,
to_json=True,
graph=output_graph)
# then
expect_zero_return_code(completed_process)
stdout = completed_process.stdout
expect = JsonGraph(json.loads(stdout))
expect.has_n_nodes(4)
expect.has_node_repr('AAACC').has_coverages_by_kmer([1, 1], [1, 1],
[2, 1])
expect.has_node_repr('C').has_coverages_by_kmer([1, 1])
expect.has_node_repr('GAA').has_coverages_by_kmer([2, 1], [1, 1],
[1, 1])
expect.has_node_repr('G').has_coverages_by_kmer([0, 1])
for color in [0, 1]:
for edge in [['AAACC', 'C'], ['C', 'GAA']]:
expect.has_repr_edge(edge[0], edge[1], color)
expect.has_repr_edge('GAA', 'G', 1)
expect.has_repr_edge('AAACC', 'GAA', 0)
expect.has_n_edges(6)
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_collapse_kmer_unitigs_option(self, tmpdir):
# given
record1 = 'AAACCCGAA'
record2 = 'ACCG'
record3 = 'TTCGGGTTT'
kmer_size = 3
output_graph = builder.Mccortex() \
.with_dna_sequence(record1) \
.with_dna_sequence(record2) \
.with_dna_sequence(record3) \
.with_kmer_size(kmer_size) \
.build(tmpdir)
runner.Mccortex(kmer_size).view(output_graph)
# when
completed_process = runner \
.Cortexpy(SPAWN_PROCESS) \
.view_contig(contig=record1,
to_json=True,
graph=output_graph)
# then
expect_zero_return_code(completed_process)
stdout = completed_process.stdout
expect = JsonGraph(json.loads(stdout))
expect.has_colors([0, 1])
expect.has_n_nodes(3)
expect.has_node_repr('AAACC').has_coverages_by_kmer([2, 1], [2, 1],
[3, 1])
expect.has_node_repr('C').has_coverages_by_kmer([2, 1])
expect.has_node_repr('GAA').has_coverages_by_kmer([3, 1], [2, 1],
[2, 1])
for edge in [('AAACC', 'C', 0), ('AAACC', 'C', 1), ('C', 'GAA', 0),
('C', 'GAA', 1), ('AAACC', 'GAA', 0)]:
expect.has_repr_edge(*edge)
expect.has_n_edges(5)
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)