def test_with_peripheral_edges_creates_unitigs(self, tmpdir):
# given
record1 = 'AAACCCGAA'
d = command.TraverseDriver(tmpdir)
d.with_json_output()
d.with_kmer_size(3)
d.with_record('ACCG')
d.with_record(record1)
d.with_record(record1 + 'G', name='sample_1')
d.with_initial_contigs('CCC')
d.with_traversal_colors(0)
# when
expect = d.run()
expect.has_node_repr('C').has_coverages_by_kmer([1, 1])
expect.has_node_repr('AAACC').has_coverages_by_kmer([1, 1], [1, 1],
[2, 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([1, 1])
expect.has_n_nodes(4)
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('AAACC', 'GAA', 0)
expect.has_repr_edge('GAA', 'G', 1)
expect.has_n_edges(6)
def test_with_initial_kmers(self, tmpdir):
# given
record1 = 'AAACCCGAA'
record2 = 'ACCG'
for query_string_idx, query_string in enumerate(
['CCC', record1, record2]):
query_dir = tmpdir / str(query_string_idx)
query_dir.ensure(dir=True)
d = command.TraverseDriver(query_dir)
d.with_records(record1, record2)
d.with_kmer_size(3)
d.with_json_output()
# when
expect = d.run()
expect.has_n_nodes(3)
expect.has_node_reprs('C', 'AAACC', 'GAA')
expect.has_node_repr('C').has_coverages_by_kmer([1])
expect.has_node_repr('AAACC').has_coverages_by_kmer([1], [1], [2])
expect.has_node_repr('GAA').has_coverages_by_kmer([2], [1], [1])
for color in [0]:
for edge in [['AAACC', 'C'], ['C', 'GAA']]:
expect.has_repr_edge(edge[0], edge[1], color)
expect.has_repr_edge('AAACC', 'GAA', 0)
expect.has_n_edges(3)
def test_of_three_colors_returns_complete_graph(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_sample_records(
'AAAT',
'AAAGG',
'CAAA',
)
d.with_kmer_size(3)
d.with_json_output()
# when
expect = d.run()
# then
expect.has_node_repr('A').has_coverages_by_color(1, 1, 1)
expect.has_node_repr('CAA').has_coverages_by_color(0, 0, 1)
expect.has_node_repr('T').has_coverages_by_color(1, 0, 0)
expect.has_node_repr('GG').has_coverages_by_color([0, 0], [1, 1],
[0, 0])
expect.has_n_nodes(4)
expect.has_node_unitig('AAA')
expect.has_node_unitig('CAA')
expect.has_node_unitig('AAT')
expect.has_node_unitig('AAGG')
expect.has_repr_edge('A', 'T', 0)
expect.has_repr_edge('A', 'GG', 1)
expect.has_repr_edge('CAA', 'A', 2)
expect.has_n_edges(3)
def test_multiple_kmers_without_seed_provides_no_output(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_records('CCCACCC')
d.with_kmer_size(3)
# when
expect = d.run()
# then
expect.has_no_records()
def test_traverses_tangle_with_non_lexlo_kmer_into_two_paths(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_kmer_size(5)
d.with_records('CAAATGGGGG', 'TAAATGGGGT')
d.with_link_records('CAAATGGGGT', 'TAAATGGGGG')
# when
expect = d.run()
# then
expect.has_records('CAAATGGGGT', 'TAAATGGGGG')
def test_traverses_two_subgraphs_into_three_records(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_records('CCCGC', 'CCCGA', 'AAAT')
d.with_kmer_size(3)
# when
expect = d.run()
# then
expect.has_record_ids('g0_p0', 'g0_p1', 'g0_p2')
expect.has_n_groups(1)
def test_traverses_two_bubbles_into_two_paths(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_kmer_size(5)
d.with_records('AACCACAAAACCCCCGAACA', 'AACCATAAAACCCCTGAACA')
d.with_link_records('AACCACAAAACCCCTGAACA', 'AACCATAAAACCCCCGAACA')
# when
expect = d.run()
# then
expect.has_records('AACCACAAAACCCCTGAACA', 'AACCATAAAACCCCCGAACA')
def test_traverses_into_two_records_with_custom_graph_idx(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_records('CCCGC', 'CCCGA')
d.with_graph_index(7)
d.with_kmer_size(3)
# when
expect = d.run()
# then
expect.has_record_ids('g7_p0', 'g7_p1')
expect.has_n_groups(1)
def test_with_non_matching_start_string_returns_empty_json(self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_json_output()
d.with_records('AAACCCGAA')
d.with_kmer_size(3)
d.with_initial_contigs('GCGC')
# when
expect = d.run()
# then
expect.has_n_nodes(0)
def test_contig_with_extra_start_kmer_that_is_start_reports_same_contig(
self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_records('ACCCAAA')
d.with_extra_start_kmer('ACC')
d.with_kmer_size(3)
# when
expect = d.run()
# then
expect.has_record('ACCCAAA')
expect.has_n_records(1)
def test_multiple_kmers_with_extra_start_kmer_reports_pseudo_linear_contig(
self, tmpdir):
# given
d = command.TraverseDriver(tmpdir)
d.with_records('CCCACCC')
d.with_extra_start_kmer('CAC')
d.with_kmer_size(3)
# when
expect = d.run()
# then
expect.has_record('CACCCA')
expect.has_n_records(1)
def test_with_revcomp_seed_kmer(self, tmpdir):
# given
record1 = 'AAACCCGAG'
record2 = 'ACCG'
query_string = 'CTC'
d = command.TraverseDriver(tmpdir)
d.with_records(record1, record2)
d.with_kmer_size(3)
d.with_seed_strings(query_string)
d.with_json_output()
# when
expect = d.run()
expect.has_node_reprs('G', 'TTT', 'CTCGG')
expect.has_node_repr('G').has_coverages_by_kmer([1])
expect.has_node_repr('TTT').has_coverages_by_kmer([2], [1], [1])
expect.has_node_repr('CTCGG').has_coverages_by_kmer([1], [1], [2])
expect.has_n_edges(3)
expect.has_repr_edge('G', 'TTT', 0)
expect.has_repr_edge('CTCGG', 'G', 0)
expect.has_repr_edge('CTCGG', 'TTT', 0)