def test_raises_when_base_that_does_not_exist_is_chosen(self):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 1 1 A', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer('AAA')
# then
with pytest.raises(KeyError):
walker.choose_branch('C')
def test_with_reverse_and_forward_link_returns_one_base_each(self, kmer):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 1 1 A', 'AAA')
b.with_link_for_kmer('R 1 1 A', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer(kmer)
# then
assert ['A'] == list(walker.next_junction_bases())
def test_with_single_link_returns_each_junctions_base(self):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 3 1 ACT', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer('AAA')
# then
assert ['A'] == list(walker.next_junction_bases())
assert ['C'] == list(walker.choose_branch('A').next_junction_bases())
assert ['T'] == list(walker.choose_branch('C').next_junction_bases())
assert [] == list(walker.choose_branch('T').next_junction_bases())
def test_with_single_link_returns_one_base(self, is_lexlo):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 3 1 ACC', 'AAA')
# when
links = b.build()
# then
junctions = list(
links.body['AAA'].get_link_junctions_in_kmer_orientation(is_lexlo))
if is_lexlo:
assert ['ACC'] == junctions
else:
assert [] == junctions
def test_y_graph_with_one_link_returns_one_node(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 1 1 C', 'AAA') \
.build()
b = UnitigBuilder()
b.add_node(0, 'AAA')
b.add_node(1, 'AAC')
b.add_node(2, 'AAG')
b.add_edge(0, 1)
b.add_edge(0, 2)
unitigs = b.build()
# when
traverser = LinkedGraphTraverser.from_graph_and_link_walker(
unitigs,
UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links, unitigs, 3, 0))
# then
for node in range(3):
assert node in traverser
assert [1] == list(traverser[0])
assert [] == list(traverser[1])
def test_two_ys_with_one_link_returns_both_nodes_the_second_time(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 1 1 C', 'AAA') \
.build()
b = UnitigBuilder()
b.add_node(0, 'AAA')
b.add_node(1, 'AACCC')
b.add_node(2, 'AAGCC')
b.add_node(3, 'CCC')
b.add_node(4, 'CCA')
b.add_node(5, 'CCT')
b.add_edge(0, 1)
b.add_edge(0, 2)
b.add_edge(1, 3)
b.add_edge(2, 3)
b.add_edge(3, 4)
b.add_edge(3, 5)
unitigs = b.build()
# when
walker = UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links, unitigs, 3, 0)
# then
assert [1] == list(walker.successors())
walker.choose(1)
assert [3] == list(walker.successors())
walker.choose(3)
assert [4, 5] == sorted(walker.successors())
walker.choose(5)
assert [] == list(walker.successors())
def test_y_graph_with_one_link_returns_one_node(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 1 1 C', 'AAA') \
.build()
b = UnitigBuilder()
b.add_node(0, 'AAA')
b.add_node(1, 'AAC')
b.add_node(2, 'AAG')
b.add_edge(0, 1)
b.add_edge(0, 2)
unitigs = b.build()
# when
walker = UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links, unitigs, 3, 0)
# then
assert [1] == list(walker.link_successors())
assert [1] == list(walker.successors())
with pytest.raises(KeyError):
walker.choose(2)
walker.choose(1)
print(list(walker.unitigs.successors(1)))
with pytest.raises(ValueError):
list(walker.link_successors())
assert [] == list(walker.successors())
def test_with_single_reverse_link_returns_one_base(self, kmer):
# given
b = LinksBuilder()
b.with_link_for_kmer('R 3 1 GTT', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer(kmer)
# then
if kmer == 'TTT':
assert 1 == walker.n_junctions
assert ['G'] == list(walker.next_junction_bases())
walker.choose_branch('G')
assert 1 == walker.n_junctions
walker.choose_branch('T')
assert 1 == walker.n_junctions
walker.choose_branch('T')
assert 0 == walker.n_junctions
else:
assert 0 == walker.n_junctions
assert [] == list(walker.next_junction_bases())
def test_with_link_for_y_graph_emits_one_path(self):
# given
b = CortexGraphBuilder()
b.with_kmer_size(3)
b.add_path('AAA', 'AAC')
b.add_path('AAA', 'AAT')
b.make_consistent('AAA')
cdb = b.build()
links = LinksBuilder() \
.with_link_for_kmer('F 1 1 C', 'AAA') \
.build()
# when
paths = list(Interactor(cdb).all_simple_paths(links=links))
# then
assert ['AAAC'] == [str(p.seq) for p in paths]
def test_bubble_and_y_with_two_links_returns_two_transcripts(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 2 1 CT', 'AAA') \
.with_link_for_kmer('F 1 1 A', 'CCC') \
.build()
b = CortexGraphBuilder()
b.with_kmer_size(3)
b.add_path('AAA', 'AAC', 'ACC', 'CCC', 'CCA')
b.add_path('AAA', 'AAG', 'AGC', 'GCC', 'CCC', 'CCT')
b.make_consistent('AAA')
cdb = b.build()
# when
paths = list(Interactor(cdb).all_simple_paths(links=links))
# then
assert ['AAACCCA', 'AAACCCT'] == sorted([str(p.seq) for p in paths])
def test_with_two_reverse_and_forward_links_returns_two_bases_each(self):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 1 1 A', 'AAA')
b.with_link_for_kmer('F 1 1 C', 'AAA')
b.with_link_for_kmer('R 1 1 G', 'AAA')
b.with_link_for_kmer('R 1 1 T', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links)
# then
assert ['A',
'C'] == list(walker.load_kmer('AAA').next_junction_bases())
assert ['G', 'T'] == list(
walker.clear().load_kmer('TTT').next_junction_bases())
def test_raises_when_link_does_match_graph(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 1 1 T', 'AAA') \
.build()
b = UnitigBuilder()
b.add_node(0, 'AAA')
b.add_node(1, 'AAC')
b.add_node(2, 'AAG')
b.add_edge(0, 1)
b.add_edge(0, 2)
unitigs = b.build()
# when
walker = UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links, unitigs, 3, 0)
# then
with pytest.raises(ValueError,
match='Links do not appear to match unitigs'):
list(walker.link_successors())
def test_two_ys_with_two_links_returns_one_and_two_nodes(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 2 1 CT', 'AAA') \
.with_link_for_kmer('F 1 1 A', 'CCC') \
.build()
b = UnitigBuilder()
b.add_node(0, 'AAA')
b.add_node(1, 'AACCC')
b.add_node(2, 'AAGCC')
b.add_node(3, 'CCC')
b.add_node(4, 'CCA')
b.add_node(5, 'CCT')
b.add_edge(0, 1)
b.add_edge(0, 2)
b.add_edge(1, 3)
b.add_edge(2, 3)
b.add_edge(3, 4)
b.add_edge(3, 5)
unitigs = b.build()
# when
walker = UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links, unitigs, 3, 0)
# then
assert [1] == list(walker.link_successors())
walker.choose(1)
with pytest.raises(ValueError):
list(walker.link_successors())
walker.choose(3)
assert [4, 5] == sorted(walker.link_successors())
walker.choose(5)
with pytest.raises(ValueError):
list(walker.link_successors())
def test_y_graph_with_one_link_returns_copy_of_walker(self):
# given
links = LinksBuilder() \
.with_link_for_kmer('F 1 1 C', 'AAA') \
.build()
b = UnitigBuilder()
b.add_node(0, 'AAA')
b.add_node(1, 'AAC')
b.add_node(2, 'AAG')
b.add_edge(0, 1)
b.add_edge(0, 2)
unitigs = b.build()
walker = UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links, unitigs, 3, 0)
# when
new_walker = copy.copy(walker)
new_walker.choose(1)
# then
assert [1] == list(walker.successors())
assert [] == list(new_walker.successors())