def test_emits_one_single_color_unitig(self):
# given
b = CortexGraphBuilder()
b.with_colors(0)
b.add_edge('AAA', 'AAT', color=0)
b.make_consistent('AAA')
graph = b.build()
# when
paths = list(Interactor(graph).all_simple_paths())
# then
assert ['AAAT'] == [str(p.seq) for p in paths]
def test_follows_two_colors_with_no_color_specified(self):
# given
b = CortexGraphBuilder()
b.with_colors(0, 1)
b.add_edge('AAA', 'AAT', color=0)
b.add_edge('AAT', 'ATA', color=1)
b.make_consistent('AAA')
graph = b.build()
# when
paths = list(Interactor(graph).all_simple_paths())
# then
assert {'AAATA'} == set([str(p.seq) for p in paths])
def test_prunes_three_tips_of_length_1_reverse_kmer(self, seed_and_expected_kmer):
# given
seed, expected_kmer = seed_and_expected_kmer
b = CortexGraphBuilder()
b.with_colors(0, 1)
kmers = ['AAC', 'ACT', 'AAG', 'CAG']
for kmer in kmers:
b.add_node(kmer)
b.add_edge(kmers[0], kmers[1], 0)
b.add_edge(kmers[0], kmers[1], 1)
b.add_edge(kmers[1], kmers[2], 0)
b.add_edge(kmers[1], kmers[3], 1)
graph = b.build()
# when
graph = interactor.Interactor(graph).prune_tips_less_than(2).graph
# then
assert 1 == len(graph)
assert {expected_kmer} == set(graph.nodes)
def test_prunes_three_tips_of_length_1(self):
# given
b = CortexGraphBuilder()
b.with_colors(0, 1)
kmers = ['AAA', 'AAC', 'ACC', 'ACG']
for kmer in kmers:
b.add_node(kmer)
b.add_edge(kmers[0], kmers[1], 0)
b.add_edge(kmers[0], kmers[1], 1)
b.add_edge(kmers[1], kmers[2], 0)
b.add_edge(kmers[1], kmers[3], 1)
graph = b.build()
# when
graph = interactor.Interactor(graph) \
.prune_tips_less_than(2) \
.graph
# then
assert 1 == len(graph)
assert {'AAC'} == set(graph.nodes)
def test_prunes_one_tip_of_length_1_in_y(self):
# given
b = CortexGraphBuilder()
b.with_colors(0, 1)
kmers = ['AAA', 'AAC', 'ACC', 'CCC', 'ACG', 'CGC']
for kmer in kmers:
b.add_node(kmer)
b.add_edge('AAA', 'AAC', 0)
b.add_edge('AAA', 'AAC', 1)
b.add_edge('AAC', 'ACC', 0)
b.add_edge('ACC', 'CCC', 0)
b.add_edge('AAC', 'ACG', 1)
b.add_edge('ACG', 'CGC', 1)
graph = b.build()
# when
graph = interactor.Interactor(graph) \
.prune_tips_less_than(2) \
.graph
# then
assert set(kmers[1:]) == set(graph.nodes)
assert 5 == len(graph)