def test_single_kmer_revcomp_seed(self, seed):
# given
b = get_cortex_builder()
b.with_kmer('AAA 1 ......G.')
b.with_kmer('AAG 1 a.......')
cdb = b.build()
# when
graph = Interactor(cdb).make_graph_nodes_consistent([seed]).graph
# then
if seed == 'AAA':
assert [] == list(graph.in_edges(seed))
assert [('AAA', 'AAG')] == list(graph.out_edges(seed))
else:
assert [('CTT', 'TTT')] == list(graph.in_edges(seed))
assert [] == list(graph.out_edges(seed))
def test_gets_correct_neighbors_of_kmer(self):
# given
b = get_cortex_builder()
b.with_kmer('AAC 1 .......T')
b.with_kmer('ACT 1 a.....G.')
b.with_kmer('CAG 1 .......T')
cdb = b.build()
seed = 'AAC'
# when
graph = Interactor(cdb).make_graph_nodes_consistent([seed]).graph
# then
assert ['CTG'] == list(graph['ACT'])
assert ['CTG'] == list(graph.succ['ACT'])
assert ['AAC'] == list(graph.pred['ACT'])
assert [('ACT', 'CTG')] == list(graph.out_edges('ACT'))
assert [('AAC', 'ACT')] == list(graph.in_edges('ACT'))
assert [] == list(graph['CTG'])
assert [] == list(graph.succ['CTG'])
assert ['ACT'] == list(graph.pred['CTG'])
assert [] == list(graph.out_edges('CTG'))
assert [('ACT', 'CTG')] == list(graph.in_edges('CTG'))