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 all_simple_paths(self, extra_incoming_node=None, links=None):
if not isinstance(self.graph, nx.Graph):
assert self.graph.is_consistent()
if extra_incoming_node:
for neighbor in self.graph.pred[extra_incoming_node]:
for color in self.graph.graph['colors']:
self.graph.remove_edge(neighbor, extra_incoming_node, color)
unitig_graph = UnitigCollapser(self.graph) \
.collapse_kmer_unitigs() \
.unitig_graph
unitig_graph = nx.DiGraph(unitig_graph)
unitig_graph = nx.convert_node_labels_to_integers(unitig_graph)
path_converter = UnitigGraphPathConverter.from_unitig_graph(unitig_graph)
record_idx = 0
in_nodes = sorted(list(in_nodes_of(unitig_graph)))
logger.info(f"Found {len(in_nodes)} incoming tip nodes")
out_nodes = set(sorted(list(out_nodes_of(unitig_graph))))
logger.info(f"Found {len(out_nodes)} outgoing tip nodes")
for sidx, source in enumerate(in_nodes):
if source in out_nodes:
logger.info('Incoming node %s; %s outgoing nodes; Path number %s',
sidx,
len(out_nodes),
record_idx)
yield SeqRecord(Seq(unitig_graph.node[source]['unitig']), id=str(record_idx),
description='')
record_idx += 1
continue
if links is not None:
wrapped_graph = LinkedGraphTraverser.from_graph_and_link_walker(
unitig_graph,
UnitigLinkWalker.from_links_unitigs_kmer_size_unitig(
links,
unitig_graph,
unitig_graph.graph['kmer_size'],
source
)
)
paths = nx.all_simple_paths(wrapped_graph,
source,
out_nodes,
cutoff=len(self.graph) - 1)
else:
paths = nx.all_simple_paths(unitig_graph,
source,
out_nodes,
cutoff=len(self.graph) - 1)
for pidx, path in enumerate(paths):
if pidx % 100000 == 0:
logger.info('Incoming node %s; %s outgoing nodes; Path number %s', sidx,
len(out_nodes), record_idx)
yield SeqRecord(
Seq(path_converter.to_contig(path)),
id=str(record_idx),
description='')
record_idx += 1
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())